[med-svn] [Git][med-team/stacks][upstream] New upstream version 2.68+dfsg
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Sat Aug 31 10:32:19 BST 2024
Étienne Mollier pushed to branch upstream at Debian Med / stacks
Commits:
f867aeed by Étienne Mollier at 2024-08-31T11:20:12+02:00
New upstream version 2.68+dfsg
- - - - -
22 changed files:
- ChangeLog
- Makefile.am
- + config/config.guess
- + config/config.sub
- configure.ac
- scripts/denovo_map.pl
- scripts/ref_map.pl
- src/PopMap.h
- src/PopSum.cc
- src/PopSum.h
- src/Vcf.cc
- src/Vcf.h
- src/clean.cc
- src/clean.h
- src/export_formats.cc
- src/export_formats.h
- src/gstacks.cc
- src/populations.cc
- src/process_radtags.cc
- src/process_radtags.h
- src/process_shortreads.cc
- src/stacks.h
Changes:
=====================================
ChangeLog
=====================================
@@ -1,3 +1,13 @@
+Stacks 2.68 - August 23, 2024
+-----------------------------
+ Bugfix: updated process_radtags so that the poly-G detection only turns on
+ automatically if --clean is also specified on the command line.
+ Bugfix: updated process_radtags so kmer length is adjusted depending on
+ adapter length; increased default kmer size to 9 from 5.
+ Bugfix: kmer coordinates were not quite right in adapter filtering after
+ removing barcodes from adapter seqeunce search, preventing adapters from
+ being properly filtered in some cases.
+
Stacks 2.67 - July 18, 2024
---------------------------
Feature: Added the --min-gt-depth filter to populations. Requires a called SNP to be supported
@@ -25,6 +35,9 @@ Stacks 2.67 - July 18, 2024
if present so as not to be duplciated after processing.
Bugfix: Corrected stacks-private-alleles to work properly with denovo
data.
+ Bugfix: Updated tsv2bam to properly assign IDs to samples that were not
+ part of the catalog. There was an off-by-one error in assigning the proper
+ IDs to these samples.
Stacks 2.66 - December 5, 2023
------------------------------
=====================================
Makefile.am
=====================================
@@ -50,6 +50,7 @@ libcore_a_SOURCES = \
libclean_a_SOURCES = \
src/clean.h src/clean.cc \
+ src/kmers.h src/kmers.cc \
src/file_io.h src/file_io.cc \
src/write.h src/write.cc
=====================================
config/config.guess
=====================================
@@ -0,0 +1,1754 @@
+#! /bin/sh
+# Attempt to guess a canonical system name.
+# Copyright 1992-2022 Free Software Foundation, Inc.
+
+# shellcheck disable=SC2006,SC2268 # see below for rationale
+
+timestamp='2022-01-09'
+
+# This file is free software; you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, see <https://www.gnu.org/licenses/>.
+#
+# As a special exception to the GNU General Public License, if you
+# distribute this file as part of a program that contains a
+# configuration script generated by Autoconf, you may include it under
+# the same distribution terms that you use for the rest of that
+# program. This Exception is an additional permission under section 7
+# of the GNU General Public License, version 3 ("GPLv3").
+#
+# Originally written by Per Bothner; maintained since 2000 by Ben Elliston.
+#
+# You can get the latest version of this script from:
+# https://git.savannah.gnu.org/cgit/config.git/plain/config.guess
+#
+# Please send patches to <config-patches at gnu.org>.
+
+
+# The "shellcheck disable" line above the timestamp inhibits complaints
+# about features and limitations of the classic Bourne shell that were
+# superseded or lifted in POSIX. However, this script identifies a wide
+# variety of pre-POSIX systems that do not have POSIX shells at all, and
+# even some reasonably current systems (Solaris 10 as case-in-point) still
+# have a pre-POSIX /bin/sh.
+
+
+me=`echo "$0" | sed -e 's,.*/,,'`
+
+usage="\
+Usage: $0 [OPTION]
+
+Output the configuration name of the system \`$me' is run on.
+
+Options:
+ -h, --help print this help, then exit
+ -t, --time-stamp print date of last modification, then exit
+ -v, --version print version number, then exit
+
+Report bugs and patches to <config-patches at gnu.org>."
+
+version="\
+GNU config.guess ($timestamp)
+
+Originally written by Per Bothner.
+Copyright 1992-2022 Free Software Foundation, Inc.
+
+This is free software; see the source for copying conditions. There is NO
+warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE."
+
+help="
+Try \`$me --help' for more information."
+
+# Parse command line
+while test $# -gt 0 ; do
+ case $1 in
+ --time-stamp | --time* | -t )
+ echo "$timestamp" ; exit ;;
+ --version | -v )
+ echo "$version" ; exit ;;
+ --help | --h* | -h )
+ echo "$usage"; exit ;;
+ -- ) # Stop option processing
+ shift; break ;;
+ - ) # Use stdin as input.
+ break ;;
+ -* )
+ echo "$me: invalid option $1$help" >&2
+ exit 1 ;;
+ * )
+ break ;;
+ esac
+done
+
+if test $# != 0; then
+ echo "$me: too many arguments$help" >&2
+ exit 1
+fi
+
+# Just in case it came from the environment.
+GUESS=
+
+# CC_FOR_BUILD -- compiler used by this script. Note that the use of a
+# compiler to aid in system detection is discouraged as it requires
+# temporary files to be created and, as you can see below, it is a
+# headache to deal with in a portable fashion.
+
+# Historically, `CC_FOR_BUILD' used to be named `HOST_CC'. We still
+# use `HOST_CC' if defined, but it is deprecated.
+
+# Portable tmp directory creation inspired by the Autoconf team.
+
+tmp=
+# shellcheck disable=SC2172
+trap 'test -z "$tmp" || rm -fr "$tmp"' 0 1 2 13 15
+
+set_cc_for_build() {
+ # prevent multiple calls if $tmp is already set
+ test "$tmp" && return 0
+ : "${TMPDIR=/tmp}"
+ # shellcheck disable=SC2039,SC3028
+ { tmp=`(umask 077 && mktemp -d "$TMPDIR/cgXXXXXX") 2>/dev/null` && test -n "$tmp" && test -d "$tmp" ; } ||
+ { test -n "$RANDOM" && tmp=$TMPDIR/cg$$-$RANDOM && (umask 077 && mkdir "$tmp" 2>/dev/null) ; } ||
+ { tmp=$TMPDIR/cg-$$ && (umask 077 && mkdir "$tmp" 2>/dev/null) && echo "Warning: creating insecure temp directory" >&2 ; } ||
+ { echo "$me: cannot create a temporary directory in $TMPDIR" >&2 ; exit 1 ; }
+ dummy=$tmp/dummy
+ case ${CC_FOR_BUILD-},${HOST_CC-},${CC-} in
+ ,,) echo "int x;" > "$dummy.c"
+ for driver in cc gcc c89 c99 ; do
+ if ($driver -c -o "$dummy.o" "$dummy.c") >/dev/null 2>&1 ; then
+ CC_FOR_BUILD=$driver
+ break
+ fi
+ done
+ if test x"$CC_FOR_BUILD" = x ; then
+ CC_FOR_BUILD=no_compiler_found
+ fi
+ ;;
+ ,,*) CC_FOR_BUILD=$CC ;;
+ ,*,*) CC_FOR_BUILD=$HOST_CC ;;
+ esac
+}
+
+# This is needed to find uname on a Pyramid OSx when run in the BSD universe.
+# (ghazi at noc.rutgers.edu 1994-08-24)
+if test -f /.attbin/uname ; then
+ PATH=$PATH:/.attbin ; export PATH
+fi
+
+UNAME_MACHINE=`(uname -m) 2>/dev/null` || UNAME_MACHINE=unknown
+UNAME_RELEASE=`(uname -r) 2>/dev/null` || UNAME_RELEASE=unknown
+UNAME_SYSTEM=`(uname -s) 2>/dev/null` || UNAME_SYSTEM=unknown
+UNAME_VERSION=`(uname -v) 2>/dev/null` || UNAME_VERSION=unknown
+
+case $UNAME_SYSTEM in
+Linux|GNU|GNU/*)
+ LIBC=unknown
+
+ set_cc_for_build
+ cat <<-EOF > "$dummy.c"
+ #include <features.h>
+ #if defined(__UCLIBC__)
+ LIBC=uclibc
+ #elif defined(__dietlibc__)
+ LIBC=dietlibc
+ #elif defined(__GLIBC__)
+ LIBC=gnu
+ #else
+ #include <stdarg.h>
+ /* First heuristic to detect musl libc. */
+ #ifdef __DEFINED_va_list
+ LIBC=musl
+ #endif
+ #endif
+ EOF
+ cc_set_libc=`$CC_FOR_BUILD -E "$dummy.c" 2>/dev/null | grep '^LIBC' | sed 's, ,,g'`
+ eval "$cc_set_libc"
+
+ # Second heuristic to detect musl libc.
+ if [ "$LIBC" = unknown ] &&
+ command -v ldd >/dev/null &&
+ ldd --version 2>&1 | grep -q ^musl; then
+ LIBC=musl
+ fi
+
+ # If the system lacks a compiler, then just pick glibc.
+ # We could probably try harder.
+ if [ "$LIBC" = unknown ]; then
+ LIBC=gnu
+ fi
+ ;;
+esac
+
+# Note: order is significant - the case branches are not exclusive.
+
+case $UNAME_MACHINE:$UNAME_SYSTEM:$UNAME_RELEASE:$UNAME_VERSION in
+ *:NetBSD:*:*)
+ # NetBSD (nbsd) targets should (where applicable) match one or
+ # more of the tuples: *-*-netbsdelf*, *-*-netbsdaout*,
+ # *-*-netbsdecoff* and *-*-netbsd*. For targets that recently
+ # switched to ELF, *-*-netbsd* would select the old
+ # object file format. This provides both forward
+ # compatibility and a consistent mechanism for selecting the
+ # object file format.
+ #
+ # Note: NetBSD doesn't particularly care about the vendor
+ # portion of the name. We always set it to "unknown".
+ UNAME_MACHINE_ARCH=`(uname -p 2>/dev/null || \
+ /sbin/sysctl -n hw.machine_arch 2>/dev/null || \
+ /usr/sbin/sysctl -n hw.machine_arch 2>/dev/null || \
+ echo unknown)`
+ case $UNAME_MACHINE_ARCH in
+ aarch64eb) machine=aarch64_be-unknown ;;
+ armeb) machine=armeb-unknown ;;
+ arm*) machine=arm-unknown ;;
+ sh3el) machine=shl-unknown ;;
+ sh3eb) machine=sh-unknown ;;
+ sh5el) machine=sh5le-unknown ;;
+ earmv*)
+ arch=`echo "$UNAME_MACHINE_ARCH" | sed -e 's,^e\(armv[0-9]\).*$,\1,'`
+ endian=`echo "$UNAME_MACHINE_ARCH" | sed -ne 's,^.*\(eb\)$,\1,p'`
+ machine=${arch}${endian}-unknown
+ ;;
+ *) machine=$UNAME_MACHINE_ARCH-unknown ;;
+ esac
+ # The Operating System including object format, if it has switched
+ # to ELF recently (or will in the future) and ABI.
+ case $UNAME_MACHINE_ARCH in
+ earm*)
+ os=netbsdelf
+ ;;
+ arm*|i386|m68k|ns32k|sh3*|sparc|vax)
+ set_cc_for_build
+ if echo __ELF__ | $CC_FOR_BUILD -E - 2>/dev/null \
+ | grep -q __ELF__
+ then
+ # Once all utilities can be ECOFF (netbsdecoff) or a.out (netbsdaout).
+ # Return netbsd for either. FIX?
+ os=netbsd
+ else
+ os=netbsdelf
+ fi
+ ;;
+ *)
+ os=netbsd
+ ;;
+ esac
+ # Determine ABI tags.
+ case $UNAME_MACHINE_ARCH in
+ earm*)
+ expr='s/^earmv[0-9]/-eabi/;s/eb$//'
+ abi=`echo "$UNAME_MACHINE_ARCH" | sed -e "$expr"`
+ ;;
+ esac
+ # The OS release
+ # Debian GNU/NetBSD machines have a different userland, and
+ # thus, need a distinct triplet. However, they do not need
+ # kernel version information, so it can be replaced with a
+ # suitable tag, in the style of linux-gnu.
+ case $UNAME_VERSION in
+ Debian*)
+ release='-gnu'
+ ;;
+ *)
+ release=`echo "$UNAME_RELEASE" | sed -e 's/[-_].*//' | cut -d. -f1,2`
+ ;;
+ esac
+ # Since CPU_TYPE-MANUFACTURER-KERNEL-OPERATING_SYSTEM:
+ # contains redundant information, the shorter form:
+ # CPU_TYPE-MANUFACTURER-OPERATING_SYSTEM is used.
+ GUESS=$machine-${os}${release}${abi-}
+ ;;
+ *:Bitrig:*:*)
+ UNAME_MACHINE_ARCH=`arch | sed 's/Bitrig.//'`
+ GUESS=$UNAME_MACHINE_ARCH-unknown-bitrig$UNAME_RELEASE
+ ;;
+ *:OpenBSD:*:*)
+ UNAME_MACHINE_ARCH=`arch | sed 's/OpenBSD.//'`
+ GUESS=$UNAME_MACHINE_ARCH-unknown-openbsd$UNAME_RELEASE
+ ;;
+ *:SecBSD:*:*)
+ UNAME_MACHINE_ARCH=`arch | sed 's/SecBSD.//'`
+ GUESS=$UNAME_MACHINE_ARCH-unknown-secbsd$UNAME_RELEASE
+ ;;
+ *:LibertyBSD:*:*)
+ UNAME_MACHINE_ARCH=`arch | sed 's/^.*BSD\.//'`
+ GUESS=$UNAME_MACHINE_ARCH-unknown-libertybsd$UNAME_RELEASE
+ ;;
+ *:MidnightBSD:*:*)
+ GUESS=$UNAME_MACHINE-unknown-midnightbsd$UNAME_RELEASE
+ ;;
+ *:ekkoBSD:*:*)
+ GUESS=$UNAME_MACHINE-unknown-ekkobsd$UNAME_RELEASE
+ ;;
+ *:SolidBSD:*:*)
+ GUESS=$UNAME_MACHINE-unknown-solidbsd$UNAME_RELEASE
+ ;;
+ *:OS108:*:*)
+ GUESS=$UNAME_MACHINE-unknown-os108_$UNAME_RELEASE
+ ;;
+ macppc:MirBSD:*:*)
+ GUESS=powerpc-unknown-mirbsd$UNAME_RELEASE
+ ;;
+ *:MirBSD:*:*)
+ GUESS=$UNAME_MACHINE-unknown-mirbsd$UNAME_RELEASE
+ ;;
+ *:Sortix:*:*)
+ GUESS=$UNAME_MACHINE-unknown-sortix
+ ;;
+ *:Twizzler:*:*)
+ GUESS=$UNAME_MACHINE-unknown-twizzler
+ ;;
+ *:Redox:*:*)
+ GUESS=$UNAME_MACHINE-unknown-redox
+ ;;
+ mips:OSF1:*.*)
+ GUESS=mips-dec-osf1
+ ;;
+ alpha:OSF1:*:*)
+ # Reset EXIT trap before exiting to avoid spurious non-zero exit code.
+ trap '' 0
+ case $UNAME_RELEASE in
+ *4.0)
+ UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $3}'`
+ ;;
+ *5.*)
+ UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $4}'`
+ ;;
+ esac
+ # According to Compaq, /usr/sbin/psrinfo has been available on
+ # OSF/1 and Tru64 systems produced since 1995. I hope that
+ # covers most systems running today. This code pipes the CPU
+ # types through head -n 1, so we only detect the type of CPU 0.
+ ALPHA_CPU_TYPE=`/usr/sbin/psrinfo -v | sed -n -e 's/^ The alpha \(.*\) processor.*$/\1/p' | head -n 1`
+ case $ALPHA_CPU_TYPE in
+ "EV4 (21064)")
+ UNAME_MACHINE=alpha ;;
+ "EV4.5 (21064)")
+ UNAME_MACHINE=alpha ;;
+ "LCA4 (21066/21068)")
+ UNAME_MACHINE=alpha ;;
+ "EV5 (21164)")
+ UNAME_MACHINE=alphaev5 ;;
+ "EV5.6 (21164A)")
+ UNAME_MACHINE=alphaev56 ;;
+ "EV5.6 (21164PC)")
+ UNAME_MACHINE=alphapca56 ;;
+ "EV5.7 (21164PC)")
+ UNAME_MACHINE=alphapca57 ;;
+ "EV6 (21264)")
+ UNAME_MACHINE=alphaev6 ;;
+ "EV6.7 (21264A)")
+ UNAME_MACHINE=alphaev67 ;;
+ "EV6.8CB (21264C)")
+ UNAME_MACHINE=alphaev68 ;;
+ "EV6.8AL (21264B)")
+ UNAME_MACHINE=alphaev68 ;;
+ "EV6.8CX (21264D)")
+ UNAME_MACHINE=alphaev68 ;;
+ "EV6.9A (21264/EV69A)")
+ UNAME_MACHINE=alphaev69 ;;
+ "EV7 (21364)")
+ UNAME_MACHINE=alphaev7 ;;
+ "EV7.9 (21364A)")
+ UNAME_MACHINE=alphaev79 ;;
+ esac
+ # A Pn.n version is a patched version.
+ # A Vn.n version is a released version.
+ # A Tn.n version is a released field test version.
+ # A Xn.n version is an unreleased experimental baselevel.
+ # 1.2 uses "1.2" for uname -r.
+ OSF_REL=`echo "$UNAME_RELEASE" | sed -e 's/^[PVTX]//' | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz`
+ GUESS=$UNAME_MACHINE-dec-osf$OSF_REL
+ ;;
+ Amiga*:UNIX_System_V:4.0:*)
+ GUESS=m68k-unknown-sysv4
+ ;;
+ *:[Aa]miga[Oo][Ss]:*:*)
+ GUESS=$UNAME_MACHINE-unknown-amigaos
+ ;;
+ *:[Mm]orph[Oo][Ss]:*:*)
+ GUESS=$UNAME_MACHINE-unknown-morphos
+ ;;
+ *:OS/390:*:*)
+ GUESS=i370-ibm-openedition
+ ;;
+ *:z/VM:*:*)
+ GUESS=s390-ibm-zvmoe
+ ;;
+ *:OS400:*:*)
+ GUESS=powerpc-ibm-os400
+ ;;
+ arm:RISC*:1.[012]*:*|arm:riscix:1.[012]*:*)
+ GUESS=arm-acorn-riscix$UNAME_RELEASE
+ ;;
+ arm*:riscos:*:*|arm*:RISCOS:*:*)
+ GUESS=arm-unknown-riscos
+ ;;
+ SR2?01:HI-UX/MPP:*:* | SR8000:HI-UX/MPP:*:*)
+ GUESS=hppa1.1-hitachi-hiuxmpp
+ ;;
+ Pyramid*:OSx*:*:* | MIS*:OSx*:*:* | MIS*:SMP_DC-OSx*:*:*)
+ # akee at wpdis03.wpafb.af.mil (Earle F. Ake) contributed MIS and NILE.
+ case `(/bin/universe) 2>/dev/null` in
+ att) GUESS=pyramid-pyramid-sysv3 ;;
+ *) GUESS=pyramid-pyramid-bsd ;;
+ esac
+ ;;
+ NILE*:*:*:dcosx)
+ GUESS=pyramid-pyramid-svr4
+ ;;
+ DRS?6000:unix:4.0:6*)
+ GUESS=sparc-icl-nx6
+ ;;
+ DRS?6000:UNIX_SV:4.2*:7* | DRS?6000:isis:4.2*:7*)
+ case `/usr/bin/uname -p` in
+ sparc) GUESS=sparc-icl-nx7 ;;
+ esac
+ ;;
+ s390x:SunOS:*:*)
+ SUN_REL=`echo "$UNAME_RELEASE" | sed -e 's/[^.]*//'`
+ GUESS=$UNAME_MACHINE-ibm-solaris2$SUN_REL
+ ;;
+ sun4H:SunOS:5.*:*)
+ SUN_REL=`echo "$UNAME_RELEASE" | sed -e 's/[^.]*//'`
+ GUESS=sparc-hal-solaris2$SUN_REL
+ ;;
+ sun4*:SunOS:5.*:* | tadpole*:SunOS:5.*:*)
+ SUN_REL=`echo "$UNAME_RELEASE" | sed -e 's/[^.]*//'`
+ GUESS=sparc-sun-solaris2$SUN_REL
+ ;;
+ i86pc:AuroraUX:5.*:* | i86xen:AuroraUX:5.*:*)
+ GUESS=i386-pc-auroraux$UNAME_RELEASE
+ ;;
+ i86pc:SunOS:5.*:* | i86xen:SunOS:5.*:*)
+ set_cc_for_build
+ SUN_ARCH=i386
+ # If there is a compiler, see if it is configured for 64-bit objects.
+ # Note that the Sun cc does not turn __LP64__ into 1 like gcc does.
+ # This test works for both compilers.
+ if test "$CC_FOR_BUILD" != no_compiler_found; then
+ if (echo '#ifdef __amd64'; echo IS_64BIT_ARCH; echo '#endif') | \
+ (CCOPTS="" $CC_FOR_BUILD -m64 -E - 2>/dev/null) | \
+ grep IS_64BIT_ARCH >/dev/null
+ then
+ SUN_ARCH=x86_64
+ fi
+ fi
+ SUN_REL=`echo "$UNAME_RELEASE" | sed -e 's/[^.]*//'`
+ GUESS=$SUN_ARCH-pc-solaris2$SUN_REL
+ ;;
+ sun4*:SunOS:6*:*)
+ # According to config.sub, this is the proper way to canonicalize
+ # SunOS6. Hard to guess exactly what SunOS6 will be like, but
+ # it's likely to be more like Solaris than SunOS4.
+ SUN_REL=`echo "$UNAME_RELEASE" | sed -e 's/[^.]*//'`
+ GUESS=sparc-sun-solaris3$SUN_REL
+ ;;
+ sun4*:SunOS:*:*)
+ case `/usr/bin/arch -k` in
+ Series*|S4*)
+ UNAME_RELEASE=`uname -v`
+ ;;
+ esac
+ # Japanese Language versions have a version number like `4.1.3-JL'.
+ SUN_REL=`echo "$UNAME_RELEASE" | sed -e 's/-/_/'`
+ GUESS=sparc-sun-sunos$SUN_REL
+ ;;
+ sun3*:SunOS:*:*)
+ GUESS=m68k-sun-sunos$UNAME_RELEASE
+ ;;
+ sun*:*:4.2BSD:*)
+ UNAME_RELEASE=`(sed 1q /etc/motd | awk '{print substr($5,1,3)}') 2>/dev/null`
+ test "x$UNAME_RELEASE" = x && UNAME_RELEASE=3
+ case `/bin/arch` in
+ sun3)
+ GUESS=m68k-sun-sunos$UNAME_RELEASE
+ ;;
+ sun4)
+ GUESS=sparc-sun-sunos$UNAME_RELEASE
+ ;;
+ esac
+ ;;
+ aushp:SunOS:*:*)
+ GUESS=sparc-auspex-sunos$UNAME_RELEASE
+ ;;
+ # The situation for MiNT is a little confusing. The machine name
+ # can be virtually everything (everything which is not
+ # "atarist" or "atariste" at least should have a processor
+ # > m68000). The system name ranges from "MiNT" over "FreeMiNT"
+ # to the lowercase version "mint" (or "freemint"). Finally
+ # the system name "TOS" denotes a system which is actually not
+ # MiNT. But MiNT is downward compatible to TOS, so this should
+ # be no problem.
+ atarist[e]:*MiNT:*:* | atarist[e]:*mint:*:* | atarist[e]:*TOS:*:*)
+ GUESS=m68k-atari-mint$UNAME_RELEASE
+ ;;
+ atari*:*MiNT:*:* | atari*:*mint:*:* | atarist[e]:*TOS:*:*)
+ GUESS=m68k-atari-mint$UNAME_RELEASE
+ ;;
+ *falcon*:*MiNT:*:* | *falcon*:*mint:*:* | *falcon*:*TOS:*:*)
+ GUESS=m68k-atari-mint$UNAME_RELEASE
+ ;;
+ milan*:*MiNT:*:* | milan*:*mint:*:* | *milan*:*TOS:*:*)
+ GUESS=m68k-milan-mint$UNAME_RELEASE
+ ;;
+ hades*:*MiNT:*:* | hades*:*mint:*:* | *hades*:*TOS:*:*)
+ GUESS=m68k-hades-mint$UNAME_RELEASE
+ ;;
+ *:*MiNT:*:* | *:*mint:*:* | *:*TOS:*:*)
+ GUESS=m68k-unknown-mint$UNAME_RELEASE
+ ;;
+ m68k:machten:*:*)
+ GUESS=m68k-apple-machten$UNAME_RELEASE
+ ;;
+ powerpc:machten:*:*)
+ GUESS=powerpc-apple-machten$UNAME_RELEASE
+ ;;
+ RISC*:Mach:*:*)
+ GUESS=mips-dec-mach_bsd4.3
+ ;;
+ RISC*:ULTRIX:*:*)
+ GUESS=mips-dec-ultrix$UNAME_RELEASE
+ ;;
+ VAX*:ULTRIX*:*:*)
+ GUESS=vax-dec-ultrix$UNAME_RELEASE
+ ;;
+ 2020:CLIX:*:* | 2430:CLIX:*:*)
+ GUESS=clipper-intergraph-clix$UNAME_RELEASE
+ ;;
+ mips:*:*:UMIPS | mips:*:*:RISCos)
+ set_cc_for_build
+ sed 's/^ //' << EOF > "$dummy.c"
+#ifdef __cplusplus
+#include <stdio.h> /* for printf() prototype */
+ int main (int argc, char *argv[]) {
+#else
+ int main (argc, argv) int argc; char *argv[]; {
+#endif
+ #if defined (host_mips) && defined (MIPSEB)
+ #if defined (SYSTYPE_SYSV)
+ printf ("mips-mips-riscos%ssysv\\n", argv[1]); exit (0);
+ #endif
+ #if defined (SYSTYPE_SVR4)
+ printf ("mips-mips-riscos%ssvr4\\n", argv[1]); exit (0);
+ #endif
+ #if defined (SYSTYPE_BSD43) || defined(SYSTYPE_BSD)
+ printf ("mips-mips-riscos%sbsd\\n", argv[1]); exit (0);
+ #endif
+ #endif
+ exit (-1);
+ }
+EOF
+ $CC_FOR_BUILD -o "$dummy" "$dummy.c" &&
+ dummyarg=`echo "$UNAME_RELEASE" | sed -n 's/\([0-9]*\).*/\1/p'` &&
+ SYSTEM_NAME=`"$dummy" "$dummyarg"` &&
+ { echo "$SYSTEM_NAME"; exit; }
+ GUESS=mips-mips-riscos$UNAME_RELEASE
+ ;;
+ Motorola:PowerMAX_OS:*:*)
+ GUESS=powerpc-motorola-powermax
+ ;;
+ Motorola:*:4.3:PL8-*)
+ GUESS=powerpc-harris-powermax
+ ;;
+ Night_Hawk:*:*:PowerMAX_OS | Synergy:PowerMAX_OS:*:*)
+ GUESS=powerpc-harris-powermax
+ ;;
+ Night_Hawk:Power_UNIX:*:*)
+ GUESS=powerpc-harris-powerunix
+ ;;
+ m88k:CX/UX:7*:*)
+ GUESS=m88k-harris-cxux7
+ ;;
+ m88k:*:4*:R4*)
+ GUESS=m88k-motorola-sysv4
+ ;;
+ m88k:*:3*:R3*)
+ GUESS=m88k-motorola-sysv3
+ ;;
+ AViiON:dgux:*:*)
+ # DG/UX returns AViiON for all architectures
+ UNAME_PROCESSOR=`/usr/bin/uname -p`
+ if test "$UNAME_PROCESSOR" = mc88100 || test "$UNAME_PROCESSOR" = mc88110
+ then
+ if test "$TARGET_BINARY_INTERFACE"x = m88kdguxelfx || \
+ test "$TARGET_BINARY_INTERFACE"x = x
+ then
+ GUESS=m88k-dg-dgux$UNAME_RELEASE
+ else
+ GUESS=m88k-dg-dguxbcs$UNAME_RELEASE
+ fi
+ else
+ GUESS=i586-dg-dgux$UNAME_RELEASE
+ fi
+ ;;
+ M88*:DolphinOS:*:*) # DolphinOS (SVR3)
+ GUESS=m88k-dolphin-sysv3
+ ;;
+ M88*:*:R3*:*)
+ # Delta 88k system running SVR3
+ GUESS=m88k-motorola-sysv3
+ ;;
+ XD88*:*:*:*) # Tektronix XD88 system running UTekV (SVR3)
+ GUESS=m88k-tektronix-sysv3
+ ;;
+ Tek43[0-9][0-9]:UTek:*:*) # Tektronix 4300 system running UTek (BSD)
+ GUESS=m68k-tektronix-bsd
+ ;;
+ *:IRIX*:*:*)
+ IRIX_REL=`echo "$UNAME_RELEASE" | sed -e 's/-/_/g'`
+ GUESS=mips-sgi-irix$IRIX_REL
+ ;;
+ ????????:AIX?:[12].1:2) # AIX 2.2.1 or AIX 2.1.1 is RT/PC AIX.
+ GUESS=romp-ibm-aix # uname -m gives an 8 hex-code CPU id
+ ;; # Note that: echo "'`uname -s`'" gives 'AIX '
+ i*86:AIX:*:*)
+ GUESS=i386-ibm-aix
+ ;;
+ ia64:AIX:*:*)
+ if test -x /usr/bin/oslevel ; then
+ IBM_REV=`/usr/bin/oslevel`
+ else
+ IBM_REV=$UNAME_VERSION.$UNAME_RELEASE
+ fi
+ GUESS=$UNAME_MACHINE-ibm-aix$IBM_REV
+ ;;
+ *:AIX:2:3)
+ if grep bos325 /usr/include/stdio.h >/dev/null 2>&1; then
+ set_cc_for_build
+ sed 's/^ //' << EOF > "$dummy.c"
+ #include <sys/systemcfg.h>
+
+ main()
+ {
+ if (!__power_pc())
+ exit(1);
+ puts("powerpc-ibm-aix3.2.5");
+ exit(0);
+ }
+EOF
+ if $CC_FOR_BUILD -o "$dummy" "$dummy.c" && SYSTEM_NAME=`"$dummy"`
+ then
+ GUESS=$SYSTEM_NAME
+ else
+ GUESS=rs6000-ibm-aix3.2.5
+ fi
+ elif grep bos324 /usr/include/stdio.h >/dev/null 2>&1; then
+ GUESS=rs6000-ibm-aix3.2.4
+ else
+ GUESS=rs6000-ibm-aix3.2
+ fi
+ ;;
+ *:AIX:*:[4567])
+ IBM_CPU_ID=`/usr/sbin/lsdev -C -c processor -S available | sed 1q | awk '{ print $1 }'`
+ if /usr/sbin/lsattr -El "$IBM_CPU_ID" | grep ' POWER' >/dev/null 2>&1; then
+ IBM_ARCH=rs6000
+ else
+ IBM_ARCH=powerpc
+ fi
+ if test -x /usr/bin/lslpp ; then
+ IBM_REV=`/usr/bin/lslpp -Lqc bos.rte.libc | \
+ awk -F: '{ print $3 }' | sed s/[0-9]*$/0/`
+ else
+ IBM_REV=$UNAME_VERSION.$UNAME_RELEASE
+ fi
+ GUESS=$IBM_ARCH-ibm-aix$IBM_REV
+ ;;
+ *:AIX:*:*)
+ GUESS=rs6000-ibm-aix
+ ;;
+ ibmrt:4.4BSD:*|romp-ibm:4.4BSD:*)
+ GUESS=romp-ibm-bsd4.4
+ ;;
+ ibmrt:*BSD:*|romp-ibm:BSD:*) # covers RT/PC BSD and
+ GUESS=romp-ibm-bsd$UNAME_RELEASE # 4.3 with uname added to
+ ;; # report: romp-ibm BSD 4.3
+ *:BOSX:*:*)
+ GUESS=rs6000-bull-bosx
+ ;;
+ DPX/2?00:B.O.S.:*:*)
+ GUESS=m68k-bull-sysv3
+ ;;
+ 9000/[34]??:4.3bsd:1.*:*)
+ GUESS=m68k-hp-bsd
+ ;;
+ hp300:4.4BSD:*:* | 9000/[34]??:4.3bsd:2.*:*)
+ GUESS=m68k-hp-bsd4.4
+ ;;
+ 9000/[34678]??:HP-UX:*:*)
+ HPUX_REV=`echo "$UNAME_RELEASE" | sed -e 's/[^.]*.[0B]*//'`
+ case $UNAME_MACHINE in
+ 9000/31?) HP_ARCH=m68000 ;;
+ 9000/[34]??) HP_ARCH=m68k ;;
+ 9000/[678][0-9][0-9])
+ if test -x /usr/bin/getconf; then
+ sc_cpu_version=`/usr/bin/getconf SC_CPU_VERSION 2>/dev/null`
+ sc_kernel_bits=`/usr/bin/getconf SC_KERNEL_BITS 2>/dev/null`
+ case $sc_cpu_version in
+ 523) HP_ARCH=hppa1.0 ;; # CPU_PA_RISC1_0
+ 528) HP_ARCH=hppa1.1 ;; # CPU_PA_RISC1_1
+ 532) # CPU_PA_RISC2_0
+ case $sc_kernel_bits in
+ 32) HP_ARCH=hppa2.0n ;;
+ 64) HP_ARCH=hppa2.0w ;;
+ '') HP_ARCH=hppa2.0 ;; # HP-UX 10.20
+ esac ;;
+ esac
+ fi
+ if test "$HP_ARCH" = ""; then
+ set_cc_for_build
+ sed 's/^ //' << EOF > "$dummy.c"
+
+ #define _HPUX_SOURCE
+ #include <stdlib.h>
+ #include <unistd.h>
+
+ int main ()
+ {
+ #if defined(_SC_KERNEL_BITS)
+ long bits = sysconf(_SC_KERNEL_BITS);
+ #endif
+ long cpu = sysconf (_SC_CPU_VERSION);
+
+ switch (cpu)
+ {
+ case CPU_PA_RISC1_0: puts ("hppa1.0"); break;
+ case CPU_PA_RISC1_1: puts ("hppa1.1"); break;
+ case CPU_PA_RISC2_0:
+ #if defined(_SC_KERNEL_BITS)
+ switch (bits)
+ {
+ case 64: puts ("hppa2.0w"); break;
+ case 32: puts ("hppa2.0n"); break;
+ default: puts ("hppa2.0"); break;
+ } break;
+ #else /* !defined(_SC_KERNEL_BITS) */
+ puts ("hppa2.0"); break;
+ #endif
+ default: puts ("hppa1.0"); break;
+ }
+ exit (0);
+ }
+EOF
+ (CCOPTS="" $CC_FOR_BUILD -o "$dummy" "$dummy.c" 2>/dev/null) && HP_ARCH=`"$dummy"`
+ test -z "$HP_ARCH" && HP_ARCH=hppa
+ fi ;;
+ esac
+ if test "$HP_ARCH" = hppa2.0w
+ then
+ set_cc_for_build
+
+ # hppa2.0w-hp-hpux* has a 64-bit kernel and a compiler generating
+ # 32-bit code. hppa64-hp-hpux* has the same kernel and a compiler
+ # generating 64-bit code. GNU and HP use different nomenclature:
+ #
+ # $ CC_FOR_BUILD=cc ./config.guess
+ # => hppa2.0w-hp-hpux11.23
+ # $ CC_FOR_BUILD="cc +DA2.0w" ./config.guess
+ # => hppa64-hp-hpux11.23
+
+ if echo __LP64__ | (CCOPTS="" $CC_FOR_BUILD -E - 2>/dev/null) |
+ grep -q __LP64__
+ then
+ HP_ARCH=hppa2.0w
+ else
+ HP_ARCH=hppa64
+ fi
+ fi
+ GUESS=$HP_ARCH-hp-hpux$HPUX_REV
+ ;;
+ ia64:HP-UX:*:*)
+ HPUX_REV=`echo "$UNAME_RELEASE" | sed -e 's/[^.]*.[0B]*//'`
+ GUESS=ia64-hp-hpux$HPUX_REV
+ ;;
+ 3050*:HI-UX:*:*)
+ set_cc_for_build
+ sed 's/^ //' << EOF > "$dummy.c"
+ #include <unistd.h>
+ int
+ main ()
+ {
+ long cpu = sysconf (_SC_CPU_VERSION);
+ /* The order matters, because CPU_IS_HP_MC68K erroneously returns
+ true for CPU_PA_RISC1_0. CPU_IS_PA_RISC returns correct
+ results, however. */
+ if (CPU_IS_PA_RISC (cpu))
+ {
+ switch (cpu)
+ {
+ case CPU_PA_RISC1_0: puts ("hppa1.0-hitachi-hiuxwe2"); break;
+ case CPU_PA_RISC1_1: puts ("hppa1.1-hitachi-hiuxwe2"); break;
+ case CPU_PA_RISC2_0: puts ("hppa2.0-hitachi-hiuxwe2"); break;
+ default: puts ("hppa-hitachi-hiuxwe2"); break;
+ }
+ }
+ else if (CPU_IS_HP_MC68K (cpu))
+ puts ("m68k-hitachi-hiuxwe2");
+ else puts ("unknown-hitachi-hiuxwe2");
+ exit (0);
+ }
+EOF
+ $CC_FOR_BUILD -o "$dummy" "$dummy.c" && SYSTEM_NAME=`"$dummy"` &&
+ { echo "$SYSTEM_NAME"; exit; }
+ GUESS=unknown-hitachi-hiuxwe2
+ ;;
+ 9000/7??:4.3bsd:*:* | 9000/8?[79]:4.3bsd:*:*)
+ GUESS=hppa1.1-hp-bsd
+ ;;
+ 9000/8??:4.3bsd:*:*)
+ GUESS=hppa1.0-hp-bsd
+ ;;
+ *9??*:MPE/iX:*:* | *3000*:MPE/iX:*:*)
+ GUESS=hppa1.0-hp-mpeix
+ ;;
+ hp7??:OSF1:*:* | hp8?[79]:OSF1:*:*)
+ GUESS=hppa1.1-hp-osf
+ ;;
+ hp8??:OSF1:*:*)
+ GUESS=hppa1.0-hp-osf
+ ;;
+ i*86:OSF1:*:*)
+ if test -x /usr/sbin/sysversion ; then
+ GUESS=$UNAME_MACHINE-unknown-osf1mk
+ else
+ GUESS=$UNAME_MACHINE-unknown-osf1
+ fi
+ ;;
+ parisc*:Lites*:*:*)
+ GUESS=hppa1.1-hp-lites
+ ;;
+ C1*:ConvexOS:*:* | convex:ConvexOS:C1*:*)
+ GUESS=c1-convex-bsd
+ ;;
+ C2*:ConvexOS:*:* | convex:ConvexOS:C2*:*)
+ if getsysinfo -f scalar_acc
+ then echo c32-convex-bsd
+ else echo c2-convex-bsd
+ fi
+ exit ;;
+ C34*:ConvexOS:*:* | convex:ConvexOS:C34*:*)
+ GUESS=c34-convex-bsd
+ ;;
+ C38*:ConvexOS:*:* | convex:ConvexOS:C38*:*)
+ GUESS=c38-convex-bsd
+ ;;
+ C4*:ConvexOS:*:* | convex:ConvexOS:C4*:*)
+ GUESS=c4-convex-bsd
+ ;;
+ CRAY*Y-MP:*:*:*)
+ CRAY_REL=`echo "$UNAME_RELEASE" | sed -e 's/\.[^.]*$/.X/'`
+ GUESS=ymp-cray-unicos$CRAY_REL
+ ;;
+ CRAY*[A-Z]90:*:*:*)
+ echo "$UNAME_MACHINE"-cray-unicos"$UNAME_RELEASE" \
+ | sed -e 's/CRAY.*\([A-Z]90\)/\1/' \
+ -e y/ABCDEFGHIJKLMNOPQRSTUVWXYZ/abcdefghijklmnopqrstuvwxyz/ \
+ -e 's/\.[^.]*$/.X/'
+ exit ;;
+ CRAY*TS:*:*:*)
+ CRAY_REL=`echo "$UNAME_RELEASE" | sed -e 's/\.[^.]*$/.X/'`
+ GUESS=t90-cray-unicos$CRAY_REL
+ ;;
+ CRAY*T3E:*:*:*)
+ CRAY_REL=`echo "$UNAME_RELEASE" | sed -e 's/\.[^.]*$/.X/'`
+ GUESS=alphaev5-cray-unicosmk$CRAY_REL
+ ;;
+ CRAY*SV1:*:*:*)
+ CRAY_REL=`echo "$UNAME_RELEASE" | sed -e 's/\.[^.]*$/.X/'`
+ GUESS=sv1-cray-unicos$CRAY_REL
+ ;;
+ *:UNICOS/mp:*:*)
+ CRAY_REL=`echo "$UNAME_RELEASE" | sed -e 's/\.[^.]*$/.X/'`
+ GUESS=craynv-cray-unicosmp$CRAY_REL
+ ;;
+ F30[01]:UNIX_System_V:*:* | F700:UNIX_System_V:*:*)
+ FUJITSU_PROC=`uname -m | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz`
+ FUJITSU_SYS=`uname -p | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz | sed -e 's/\///'`
+ FUJITSU_REL=`echo "$UNAME_RELEASE" | sed -e 's/ /_/'`
+ GUESS=${FUJITSU_PROC}-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}
+ ;;
+ 5000:UNIX_System_V:4.*:*)
+ FUJITSU_SYS=`uname -p | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz | sed -e 's/\///'`
+ FUJITSU_REL=`echo "$UNAME_RELEASE" | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz | sed -e 's/ /_/'`
+ GUESS=sparc-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}
+ ;;
+ i*86:BSD/386:*:* | i*86:BSD/OS:*:* | *:Ascend\ Embedded/OS:*:*)
+ GUESS=$UNAME_MACHINE-pc-bsdi$UNAME_RELEASE
+ ;;
+ sparc*:BSD/OS:*:*)
+ GUESS=sparc-unknown-bsdi$UNAME_RELEASE
+ ;;
+ *:BSD/OS:*:*)
+ GUESS=$UNAME_MACHINE-unknown-bsdi$UNAME_RELEASE
+ ;;
+ arm:FreeBSD:*:*)
+ UNAME_PROCESSOR=`uname -p`
+ set_cc_for_build
+ if echo __ARM_PCS_VFP | $CC_FOR_BUILD -E - 2>/dev/null \
+ | grep -q __ARM_PCS_VFP
+ then
+ FREEBSD_REL=`echo "$UNAME_RELEASE" | sed -e 's/[-(].*//'`
+ GUESS=$UNAME_PROCESSOR-unknown-freebsd$FREEBSD_REL-gnueabi
+ else
+ FREEBSD_REL=`echo "$UNAME_RELEASE" | sed -e 's/[-(].*//'`
+ GUESS=$UNAME_PROCESSOR-unknown-freebsd$FREEBSD_REL-gnueabihf
+ fi
+ ;;
+ *:FreeBSD:*:*)
+ UNAME_PROCESSOR=`/usr/bin/uname -p`
+ case $UNAME_PROCESSOR in
+ amd64)
+ UNAME_PROCESSOR=x86_64 ;;
+ i386)
+ UNAME_PROCESSOR=i586 ;;
+ esac
+ FREEBSD_REL=`echo "$UNAME_RELEASE" | sed -e 's/[-(].*//'`
+ GUESS=$UNAME_PROCESSOR-unknown-freebsd$FREEBSD_REL
+ ;;
+ i*:CYGWIN*:*)
+ GUESS=$UNAME_MACHINE-pc-cygwin
+ ;;
+ *:MINGW64*:*)
+ GUESS=$UNAME_MACHINE-pc-mingw64
+ ;;
+ *:MINGW*:*)
+ GUESS=$UNAME_MACHINE-pc-mingw32
+ ;;
+ *:MSYS*:*)
+ GUESS=$UNAME_MACHINE-pc-msys
+ ;;
+ i*:PW*:*)
+ GUESS=$UNAME_MACHINE-pc-pw32
+ ;;
+ *:SerenityOS:*:*)
+ GUESS=$UNAME_MACHINE-pc-serenity
+ ;;
+ *:Interix*:*)
+ case $UNAME_MACHINE in
+ x86)
+ GUESS=i586-pc-interix$UNAME_RELEASE
+ ;;
+ authenticamd | genuineintel | EM64T)
+ GUESS=x86_64-unknown-interix$UNAME_RELEASE
+ ;;
+ IA64)
+ GUESS=ia64-unknown-interix$UNAME_RELEASE
+ ;;
+ esac ;;
+ i*:UWIN*:*)
+ GUESS=$UNAME_MACHINE-pc-uwin
+ ;;
+ amd64:CYGWIN*:*:* | x86_64:CYGWIN*:*:*)
+ GUESS=x86_64-pc-cygwin
+ ;;
+ prep*:SunOS:5.*:*)
+ SUN_REL=`echo "$UNAME_RELEASE" | sed -e 's/[^.]*//'`
+ GUESS=powerpcle-unknown-solaris2$SUN_REL
+ ;;
+ *:GNU:*:*)
+ # the GNU system
+ GNU_ARCH=`echo "$UNAME_MACHINE" | sed -e 's,[-/].*$,,'`
+ GNU_REL=`echo "$UNAME_RELEASE" | sed -e 's,/.*$,,'`
+ GUESS=$GNU_ARCH-unknown-$LIBC$GNU_REL
+ ;;
+ *:GNU/*:*:*)
+ # other systems with GNU libc and userland
+ GNU_SYS=`echo "$UNAME_SYSTEM" | sed 's,^[^/]*/,,' | tr "[:upper:]" "[:lower:]"`
+ GNU_REL=`echo "$UNAME_RELEASE" | sed -e 's/[-(].*//'`
+ GUESS=$UNAME_MACHINE-unknown-$GNU_SYS$GNU_REL-$LIBC
+ ;;
+ *:Minix:*:*)
+ GUESS=$UNAME_MACHINE-unknown-minix
+ ;;
+ aarch64:Linux:*:*)
+ GUESS=$UNAME_MACHINE-unknown-linux-$LIBC
+ ;;
+ aarch64_be:Linux:*:*)
+ UNAME_MACHINE=aarch64_be
+ GUESS=$UNAME_MACHINE-unknown-linux-$LIBC
+ ;;
+ alpha:Linux:*:*)
+ case `sed -n '/^cpu model/s/^.*: \(.*\)/\1/p' /proc/cpuinfo 2>/dev/null` in
+ EV5) UNAME_MACHINE=alphaev5 ;;
+ EV56) UNAME_MACHINE=alphaev56 ;;
+ PCA56) UNAME_MACHINE=alphapca56 ;;
+ PCA57) UNAME_MACHINE=alphapca56 ;;
+ EV6) UNAME_MACHINE=alphaev6 ;;
+ EV67) UNAME_MACHINE=alphaev67 ;;
+ EV68*) UNAME_MACHINE=alphaev68 ;;
+ esac
+ objdump --private-headers /bin/sh | grep -q ld.so.1
+ if test "$?" = 0 ; then LIBC=gnulibc1 ; fi
+ GUESS=$UNAME_MACHINE-unknown-linux-$LIBC
+ ;;
+ arc:Linux:*:* | arceb:Linux:*:* | arc32:Linux:*:* | arc64:Linux:*:*)
+ GUESS=$UNAME_MACHINE-unknown-linux-$LIBC
+ ;;
+ arm*:Linux:*:*)
+ set_cc_for_build
+ if echo __ARM_EABI__ | $CC_FOR_BUILD -E - 2>/dev/null \
+ | grep -q __ARM_EABI__
+ then
+ GUESS=$UNAME_MACHINE-unknown-linux-$LIBC
+ else
+ if echo __ARM_PCS_VFP | $CC_FOR_BUILD -E - 2>/dev/null \
+ | grep -q __ARM_PCS_VFP
+ then
+ GUESS=$UNAME_MACHINE-unknown-linux-${LIBC}eabi
+ else
+ GUESS=$UNAME_MACHINE-unknown-linux-${LIBC}eabihf
+ fi
+ fi
+ ;;
+ avr32*:Linux:*:*)
+ GUESS=$UNAME_MACHINE-unknown-linux-$LIBC
+ ;;
+ cris:Linux:*:*)
+ GUESS=$UNAME_MACHINE-axis-linux-$LIBC
+ ;;
+ crisv32:Linux:*:*)
+ GUESS=$UNAME_MACHINE-axis-linux-$LIBC
+ ;;
+ e2k:Linux:*:*)
+ GUESS=$UNAME_MACHINE-unknown-linux-$LIBC
+ ;;
+ frv:Linux:*:*)
+ GUESS=$UNAME_MACHINE-unknown-linux-$LIBC
+ ;;
+ hexagon:Linux:*:*)
+ GUESS=$UNAME_MACHINE-unknown-linux-$LIBC
+ ;;
+ i*86:Linux:*:*)
+ GUESS=$UNAME_MACHINE-pc-linux-$LIBC
+ ;;
+ ia64:Linux:*:*)
+ GUESS=$UNAME_MACHINE-unknown-linux-$LIBC
+ ;;
+ k1om:Linux:*:*)
+ GUESS=$UNAME_MACHINE-unknown-linux-$LIBC
+ ;;
+ loongarch32:Linux:*:* | loongarch64:Linux:*:* | loongarchx32:Linux:*:*)
+ GUESS=$UNAME_MACHINE-unknown-linux-$LIBC
+ ;;
+ m32r*:Linux:*:*)
+ GUESS=$UNAME_MACHINE-unknown-linux-$LIBC
+ ;;
+ m68*:Linux:*:*)
+ GUESS=$UNAME_MACHINE-unknown-linux-$LIBC
+ ;;
+ mips:Linux:*:* | mips64:Linux:*:*)
+ set_cc_for_build
+ IS_GLIBC=0
+ test x"${LIBC}" = xgnu && IS_GLIBC=1
+ sed 's/^ //' << EOF > "$dummy.c"
+ #undef CPU
+ #undef mips
+ #undef mipsel
+ #undef mips64
+ #undef mips64el
+ #if ${IS_GLIBC} && defined(_ABI64)
+ LIBCABI=gnuabi64
+ #else
+ #if ${IS_GLIBC} && defined(_ABIN32)
+ LIBCABI=gnuabin32
+ #else
+ LIBCABI=${LIBC}
+ #endif
+ #endif
+
+ #if ${IS_GLIBC} && defined(__mips64) && defined(__mips_isa_rev) && __mips_isa_rev>=6
+ CPU=mipsisa64r6
+ #else
+ #if ${IS_GLIBC} && !defined(__mips64) && defined(__mips_isa_rev) && __mips_isa_rev>=6
+ CPU=mipsisa32r6
+ #else
+ #if defined(__mips64)
+ CPU=mips64
+ #else
+ CPU=mips
+ #endif
+ #endif
+ #endif
+
+ #if defined(__MIPSEL__) || defined(__MIPSEL) || defined(_MIPSEL) || defined(MIPSEL)
+ MIPS_ENDIAN=el
+ #else
+ #if defined(__MIPSEB__) || defined(__MIPSEB) || defined(_MIPSEB) || defined(MIPSEB)
+ MIPS_ENDIAN=
+ #else
+ MIPS_ENDIAN=
+ #endif
+ #endif
+EOF
+ cc_set_vars=`$CC_FOR_BUILD -E "$dummy.c" 2>/dev/null | grep '^CPU\|^MIPS_ENDIAN\|^LIBCABI'`
+ eval "$cc_set_vars"
+ test "x$CPU" != x && { echo "$CPU${MIPS_ENDIAN}-unknown-linux-$LIBCABI"; exit; }
+ ;;
+ mips64el:Linux:*:*)
+ GUESS=$UNAME_MACHINE-unknown-linux-$LIBC
+ ;;
+ openrisc*:Linux:*:*)
+ GUESS=or1k-unknown-linux-$LIBC
+ ;;
+ or32:Linux:*:* | or1k*:Linux:*:*)
+ GUESS=$UNAME_MACHINE-unknown-linux-$LIBC
+ ;;
+ padre:Linux:*:*)
+ GUESS=sparc-unknown-linux-$LIBC
+ ;;
+ parisc64:Linux:*:* | hppa64:Linux:*:*)
+ GUESS=hppa64-unknown-linux-$LIBC
+ ;;
+ parisc:Linux:*:* | hppa:Linux:*:*)
+ # Look for CPU level
+ case `grep '^cpu[^a-z]*:' /proc/cpuinfo 2>/dev/null | cut -d' ' -f2` in
+ PA7*) GUESS=hppa1.1-unknown-linux-$LIBC ;;
+ PA8*) GUESS=hppa2.0-unknown-linux-$LIBC ;;
+ *) GUESS=hppa-unknown-linux-$LIBC ;;
+ esac
+ ;;
+ ppc64:Linux:*:*)
+ GUESS=powerpc64-unknown-linux-$LIBC
+ ;;
+ ppc:Linux:*:*)
+ GUESS=powerpc-unknown-linux-$LIBC
+ ;;
+ ppc64le:Linux:*:*)
+ GUESS=powerpc64le-unknown-linux-$LIBC
+ ;;
+ ppcle:Linux:*:*)
+ GUESS=powerpcle-unknown-linux-$LIBC
+ ;;
+ riscv32:Linux:*:* | riscv32be:Linux:*:* | riscv64:Linux:*:* | riscv64be:Linux:*:*)
+ GUESS=$UNAME_MACHINE-unknown-linux-$LIBC
+ ;;
+ s390:Linux:*:* | s390x:Linux:*:*)
+ GUESS=$UNAME_MACHINE-ibm-linux-$LIBC
+ ;;
+ sh64*:Linux:*:*)
+ GUESS=$UNAME_MACHINE-unknown-linux-$LIBC
+ ;;
+ sh*:Linux:*:*)
+ GUESS=$UNAME_MACHINE-unknown-linux-$LIBC
+ ;;
+ sparc:Linux:*:* | sparc64:Linux:*:*)
+ GUESS=$UNAME_MACHINE-unknown-linux-$LIBC
+ ;;
+ tile*:Linux:*:*)
+ GUESS=$UNAME_MACHINE-unknown-linux-$LIBC
+ ;;
+ vax:Linux:*:*)
+ GUESS=$UNAME_MACHINE-dec-linux-$LIBC
+ ;;
+ x86_64:Linux:*:*)
+ set_cc_for_build
+ LIBCABI=$LIBC
+ if test "$CC_FOR_BUILD" != no_compiler_found; then
+ if (echo '#ifdef __ILP32__'; echo IS_X32; echo '#endif') | \
+ (CCOPTS="" $CC_FOR_BUILD -E - 2>/dev/null) | \
+ grep IS_X32 >/dev/null
+ then
+ LIBCABI=${LIBC}x32
+ fi
+ fi
+ GUESS=$UNAME_MACHINE-pc-linux-$LIBCABI
+ ;;
+ xtensa*:Linux:*:*)
+ GUESS=$UNAME_MACHINE-unknown-linux-$LIBC
+ ;;
+ i*86:DYNIX/ptx:4*:*)
+ # ptx 4.0 does uname -s correctly, with DYNIX/ptx in there.
+ # earlier versions are messed up and put the nodename in both
+ # sysname and nodename.
+ GUESS=i386-sequent-sysv4
+ ;;
+ i*86:UNIX_SV:4.2MP:2.*)
+ # Unixware is an offshoot of SVR4, but it has its own version
+ # number series starting with 2...
+ # I am not positive that other SVR4 systems won't match this,
+ # I just have to hope. -- rms.
+ # Use sysv4.2uw... so that sysv4* matches it.
+ GUESS=$UNAME_MACHINE-pc-sysv4.2uw$UNAME_VERSION
+ ;;
+ i*86:OS/2:*:*)
+ # If we were able to find `uname', then EMX Unix compatibility
+ # is probably installed.
+ GUESS=$UNAME_MACHINE-pc-os2-emx
+ ;;
+ i*86:XTS-300:*:STOP)
+ GUESS=$UNAME_MACHINE-unknown-stop
+ ;;
+ i*86:atheos:*:*)
+ GUESS=$UNAME_MACHINE-unknown-atheos
+ ;;
+ i*86:syllable:*:*)
+ GUESS=$UNAME_MACHINE-pc-syllable
+ ;;
+ i*86:LynxOS:2.*:* | i*86:LynxOS:3.[01]*:* | i*86:LynxOS:4.[02]*:*)
+ GUESS=i386-unknown-lynxos$UNAME_RELEASE
+ ;;
+ i*86:*DOS:*:*)
+ GUESS=$UNAME_MACHINE-pc-msdosdjgpp
+ ;;
+ i*86:*:4.*:*)
+ UNAME_REL=`echo "$UNAME_RELEASE" | sed 's/\/MP$//'`
+ if grep Novell /usr/include/link.h >/dev/null 2>/dev/null; then
+ GUESS=$UNAME_MACHINE-univel-sysv$UNAME_REL
+ else
+ GUESS=$UNAME_MACHINE-pc-sysv$UNAME_REL
+ fi
+ ;;
+ i*86:*:5:[678]*)
+ # UnixWare 7.x, OpenUNIX and OpenServer 6.
+ case `/bin/uname -X | grep "^Machine"` in
+ *486*) UNAME_MACHINE=i486 ;;
+ *Pentium) UNAME_MACHINE=i586 ;;
+ *Pent*|*Celeron) UNAME_MACHINE=i686 ;;
+ esac
+ GUESS=$UNAME_MACHINE-unknown-sysv${UNAME_RELEASE}${UNAME_SYSTEM}${UNAME_VERSION}
+ ;;
+ i*86:*:3.2:*)
+ if test -f /usr/options/cb.name; then
+ UNAME_REL=`sed -n 's/.*Version //p' </usr/options/cb.name`
+ GUESS=$UNAME_MACHINE-pc-isc$UNAME_REL
+ elif /bin/uname -X 2>/dev/null >/dev/null ; then
+ UNAME_REL=`(/bin/uname -X|grep Release|sed -e 's/.*= //')`
+ (/bin/uname -X|grep i80486 >/dev/null) && UNAME_MACHINE=i486
+ (/bin/uname -X|grep '^Machine.*Pentium' >/dev/null) \
+ && UNAME_MACHINE=i586
+ (/bin/uname -X|grep '^Machine.*Pent *II' >/dev/null) \
+ && UNAME_MACHINE=i686
+ (/bin/uname -X|grep '^Machine.*Pentium Pro' >/dev/null) \
+ && UNAME_MACHINE=i686
+ GUESS=$UNAME_MACHINE-pc-sco$UNAME_REL
+ else
+ GUESS=$UNAME_MACHINE-pc-sysv32
+ fi
+ ;;
+ pc:*:*:*)
+ # Left here for compatibility:
+ # uname -m prints for DJGPP always 'pc', but it prints nothing about
+ # the processor, so we play safe by assuming i586.
+ # Note: whatever this is, it MUST be the same as what config.sub
+ # prints for the "djgpp" host, or else GDB configure will decide that
+ # this is a cross-build.
+ GUESS=i586-pc-msdosdjgpp
+ ;;
+ Intel:Mach:3*:*)
+ GUESS=i386-pc-mach3
+ ;;
+ paragon:*:*:*)
+ GUESS=i860-intel-osf1
+ ;;
+ i860:*:4.*:*) # i860-SVR4
+ if grep Stardent /usr/include/sys/uadmin.h >/dev/null 2>&1 ; then
+ GUESS=i860-stardent-sysv$UNAME_RELEASE # Stardent Vistra i860-SVR4
+ else # Add other i860-SVR4 vendors below as they are discovered.
+ GUESS=i860-unknown-sysv$UNAME_RELEASE # Unknown i860-SVR4
+ fi
+ ;;
+ mini*:CTIX:SYS*5:*)
+ # "miniframe"
+ GUESS=m68010-convergent-sysv
+ ;;
+ mc68k:UNIX:SYSTEM5:3.51m)
+ GUESS=m68k-convergent-sysv
+ ;;
+ M680?0:D-NIX:5.3:*)
+ GUESS=m68k-diab-dnix
+ ;;
+ M68*:*:R3V[5678]*:*)
+ test -r /sysV68 && { echo 'm68k-motorola-sysv'; exit; } ;;
+ 3[345]??:*:4.0:3.0 | 3[34]??A:*:4.0:3.0 | 3[34]??,*:*:4.0:3.0 | 3[34]??/*:*:4.0:3.0 | 4400:*:4.0:3.0 | 4850:*:4.0:3.0 | SKA40:*:4.0:3.0 | SDS2:*:4.0:3.0 | SHG2:*:4.0:3.0 | S7501*:*:4.0:3.0)
+ OS_REL=''
+ test -r /etc/.relid \
+ && OS_REL=.`sed -n 's/[^ ]* [^ ]* \([0-9][0-9]\).*/\1/p' < /etc/.relid`
+ /bin/uname -p 2>/dev/null | grep 86 >/dev/null \
+ && { echo i486-ncr-sysv4.3"$OS_REL"; exit; }
+ /bin/uname -p 2>/dev/null | /bin/grep entium >/dev/null \
+ && { echo i586-ncr-sysv4.3"$OS_REL"; exit; } ;;
+ 3[34]??:*:4.0:* | 3[34]??,*:*:4.0:*)
+ /bin/uname -p 2>/dev/null | grep 86 >/dev/null \
+ && { echo i486-ncr-sysv4; exit; } ;;
+ NCR*:*:4.2:* | MPRAS*:*:4.2:*)
+ OS_REL='.3'
+ test -r /etc/.relid \
+ && OS_REL=.`sed -n 's/[^ ]* [^ ]* \([0-9][0-9]\).*/\1/p' < /etc/.relid`
+ /bin/uname -p 2>/dev/null | grep 86 >/dev/null \
+ && { echo i486-ncr-sysv4.3"$OS_REL"; exit; }
+ /bin/uname -p 2>/dev/null | /bin/grep entium >/dev/null \
+ && { echo i586-ncr-sysv4.3"$OS_REL"; exit; }
+ /bin/uname -p 2>/dev/null | /bin/grep pteron >/dev/null \
+ && { echo i586-ncr-sysv4.3"$OS_REL"; exit; } ;;
+ m68*:LynxOS:2.*:* | m68*:LynxOS:3.0*:*)
+ GUESS=m68k-unknown-lynxos$UNAME_RELEASE
+ ;;
+ mc68030:UNIX_System_V:4.*:*)
+ GUESS=m68k-atari-sysv4
+ ;;
+ TSUNAMI:LynxOS:2.*:*)
+ GUESS=sparc-unknown-lynxos$UNAME_RELEASE
+ ;;
+ rs6000:LynxOS:2.*:*)
+ GUESS=rs6000-unknown-lynxos$UNAME_RELEASE
+ ;;
+ PowerPC:LynxOS:2.*:* | PowerPC:LynxOS:3.[01]*:* | PowerPC:LynxOS:4.[02]*:*)
+ GUESS=powerpc-unknown-lynxos$UNAME_RELEASE
+ ;;
+ SM[BE]S:UNIX_SV:*:*)
+ GUESS=mips-dde-sysv$UNAME_RELEASE
+ ;;
+ RM*:ReliantUNIX-*:*:*)
+ GUESS=mips-sni-sysv4
+ ;;
+ RM*:SINIX-*:*:*)
+ GUESS=mips-sni-sysv4
+ ;;
+ *:SINIX-*:*:*)
+ if uname -p 2>/dev/null >/dev/null ; then
+ UNAME_MACHINE=`(uname -p) 2>/dev/null`
+ GUESS=$UNAME_MACHINE-sni-sysv4
+ else
+ GUESS=ns32k-sni-sysv
+ fi
+ ;;
+ PENTIUM:*:4.0*:*) # Unisys `ClearPath HMP IX 4000' SVR4/MP effort
+ # says <Richard.M.Bartel at ccMail.Census.GOV>
+ GUESS=i586-unisys-sysv4
+ ;;
+ *:UNIX_System_V:4*:FTX*)
+ # From Gerald Hewes <hewes at openmarket.com>.
+ # How about differentiating between stratus architectures? -djm
+ GUESS=hppa1.1-stratus-sysv4
+ ;;
+ *:*:*:FTX*)
+ # From seanf at swdc.stratus.com.
+ GUESS=i860-stratus-sysv4
+ ;;
+ i*86:VOS:*:*)
+ # From Paul.Green at stratus.com.
+ GUESS=$UNAME_MACHINE-stratus-vos
+ ;;
+ *:VOS:*:*)
+ # From Paul.Green at stratus.com.
+ GUESS=hppa1.1-stratus-vos
+ ;;
+ mc68*:A/UX:*:*)
+ GUESS=m68k-apple-aux$UNAME_RELEASE
+ ;;
+ news*:NEWS-OS:6*:*)
+ GUESS=mips-sony-newsos6
+ ;;
+ R[34]000:*System_V*:*:* | R4000:UNIX_SYSV:*:* | R*000:UNIX_SV:*:*)
+ if test -d /usr/nec; then
+ GUESS=mips-nec-sysv$UNAME_RELEASE
+ else
+ GUESS=mips-unknown-sysv$UNAME_RELEASE
+ fi
+ ;;
+ BeBox:BeOS:*:*) # BeOS running on hardware made by Be, PPC only.
+ GUESS=powerpc-be-beos
+ ;;
+ BeMac:BeOS:*:*) # BeOS running on Mac or Mac clone, PPC only.
+ GUESS=powerpc-apple-beos
+ ;;
+ BePC:BeOS:*:*) # BeOS running on Intel PC compatible.
+ GUESS=i586-pc-beos
+ ;;
+ BePC:Haiku:*:*) # Haiku running on Intel PC compatible.
+ GUESS=i586-pc-haiku
+ ;;
+ x86_64:Haiku:*:*)
+ GUESS=x86_64-unknown-haiku
+ ;;
+ SX-4:SUPER-UX:*:*)
+ GUESS=sx4-nec-superux$UNAME_RELEASE
+ ;;
+ SX-5:SUPER-UX:*:*)
+ GUESS=sx5-nec-superux$UNAME_RELEASE
+ ;;
+ SX-6:SUPER-UX:*:*)
+ GUESS=sx6-nec-superux$UNAME_RELEASE
+ ;;
+ SX-7:SUPER-UX:*:*)
+ GUESS=sx7-nec-superux$UNAME_RELEASE
+ ;;
+ SX-8:SUPER-UX:*:*)
+ GUESS=sx8-nec-superux$UNAME_RELEASE
+ ;;
+ SX-8R:SUPER-UX:*:*)
+ GUESS=sx8r-nec-superux$UNAME_RELEASE
+ ;;
+ SX-ACE:SUPER-UX:*:*)
+ GUESS=sxace-nec-superux$UNAME_RELEASE
+ ;;
+ Power*:Rhapsody:*:*)
+ GUESS=powerpc-apple-rhapsody$UNAME_RELEASE
+ ;;
+ *:Rhapsody:*:*)
+ GUESS=$UNAME_MACHINE-apple-rhapsody$UNAME_RELEASE
+ ;;
+ arm64:Darwin:*:*)
+ GUESS=aarch64-apple-darwin$UNAME_RELEASE
+ ;;
+ *:Darwin:*:*)
+ UNAME_PROCESSOR=`uname -p`
+ case $UNAME_PROCESSOR in
+ unknown) UNAME_PROCESSOR=powerpc ;;
+ esac
+ if command -v xcode-select > /dev/null 2> /dev/null && \
+ ! xcode-select --print-path > /dev/null 2> /dev/null ; then
+ # Avoid executing cc if there is no toolchain installed as
+ # cc will be a stub that puts up a graphical alert
+ # prompting the user to install developer tools.
+ CC_FOR_BUILD=no_compiler_found
+ else
+ set_cc_for_build
+ fi
+ if test "$CC_FOR_BUILD" != no_compiler_found; then
+ if (echo '#ifdef __LP64__'; echo IS_64BIT_ARCH; echo '#endif') | \
+ (CCOPTS="" $CC_FOR_BUILD -E - 2>/dev/null) | \
+ grep IS_64BIT_ARCH >/dev/null
+ then
+ case $UNAME_PROCESSOR in
+ i386) UNAME_PROCESSOR=x86_64 ;;
+ powerpc) UNAME_PROCESSOR=powerpc64 ;;
+ esac
+ fi
+ # On 10.4-10.6 one might compile for PowerPC via gcc -arch ppc
+ if (echo '#ifdef __POWERPC__'; echo IS_PPC; echo '#endif') | \
+ (CCOPTS="" $CC_FOR_BUILD -E - 2>/dev/null) | \
+ grep IS_PPC >/dev/null
+ then
+ UNAME_PROCESSOR=powerpc
+ fi
+ elif test "$UNAME_PROCESSOR" = i386 ; then
+ # uname -m returns i386 or x86_64
+ UNAME_PROCESSOR=$UNAME_MACHINE
+ fi
+ GUESS=$UNAME_PROCESSOR-apple-darwin$UNAME_RELEASE
+ ;;
+ *:procnto*:*:* | *:QNX:[0123456789]*:*)
+ UNAME_PROCESSOR=`uname -p`
+ if test "$UNAME_PROCESSOR" = x86; then
+ UNAME_PROCESSOR=i386
+ UNAME_MACHINE=pc
+ fi
+ GUESS=$UNAME_PROCESSOR-$UNAME_MACHINE-nto-qnx$UNAME_RELEASE
+ ;;
+ *:QNX:*:4*)
+ GUESS=i386-pc-qnx
+ ;;
+ NEO-*:NONSTOP_KERNEL:*:*)
+ GUESS=neo-tandem-nsk$UNAME_RELEASE
+ ;;
+ NSE-*:NONSTOP_KERNEL:*:*)
+ GUESS=nse-tandem-nsk$UNAME_RELEASE
+ ;;
+ NSR-*:NONSTOP_KERNEL:*:*)
+ GUESS=nsr-tandem-nsk$UNAME_RELEASE
+ ;;
+ NSV-*:NONSTOP_KERNEL:*:*)
+ GUESS=nsv-tandem-nsk$UNAME_RELEASE
+ ;;
+ NSX-*:NONSTOP_KERNEL:*:*)
+ GUESS=nsx-tandem-nsk$UNAME_RELEASE
+ ;;
+ *:NonStop-UX:*:*)
+ GUESS=mips-compaq-nonstopux
+ ;;
+ BS2000:POSIX*:*:*)
+ GUESS=bs2000-siemens-sysv
+ ;;
+ DS/*:UNIX_System_V:*:*)
+ GUESS=$UNAME_MACHINE-$UNAME_SYSTEM-$UNAME_RELEASE
+ ;;
+ *:Plan9:*:*)
+ # "uname -m" is not consistent, so use $cputype instead. 386
+ # is converted to i386 for consistency with other x86
+ # operating systems.
+ if test "${cputype-}" = 386; then
+ UNAME_MACHINE=i386
+ elif test "x${cputype-}" != x; then
+ UNAME_MACHINE=$cputype
+ fi
+ GUESS=$UNAME_MACHINE-unknown-plan9
+ ;;
+ *:TOPS-10:*:*)
+ GUESS=pdp10-unknown-tops10
+ ;;
+ *:TENEX:*:*)
+ GUESS=pdp10-unknown-tenex
+ ;;
+ KS10:TOPS-20:*:* | KL10:TOPS-20:*:* | TYPE4:TOPS-20:*:*)
+ GUESS=pdp10-dec-tops20
+ ;;
+ XKL-1:TOPS-20:*:* | TYPE5:TOPS-20:*:*)
+ GUESS=pdp10-xkl-tops20
+ ;;
+ *:TOPS-20:*:*)
+ GUESS=pdp10-unknown-tops20
+ ;;
+ *:ITS:*:*)
+ GUESS=pdp10-unknown-its
+ ;;
+ SEI:*:*:SEIUX)
+ GUESS=mips-sei-seiux$UNAME_RELEASE
+ ;;
+ *:DragonFly:*:*)
+ DRAGONFLY_REL=`echo "$UNAME_RELEASE" | sed -e 's/[-(].*//'`
+ GUESS=$UNAME_MACHINE-unknown-dragonfly$DRAGONFLY_REL
+ ;;
+ *:*VMS:*:*)
+ UNAME_MACHINE=`(uname -p) 2>/dev/null`
+ case $UNAME_MACHINE in
+ A*) GUESS=alpha-dec-vms ;;
+ I*) GUESS=ia64-dec-vms ;;
+ V*) GUESS=vax-dec-vms ;;
+ esac ;;
+ *:XENIX:*:SysV)
+ GUESS=i386-pc-xenix
+ ;;
+ i*86:skyos:*:*)
+ SKYOS_REL=`echo "$UNAME_RELEASE" | sed -e 's/ .*$//'`
+ GUESS=$UNAME_MACHINE-pc-skyos$SKYOS_REL
+ ;;
+ i*86:rdos:*:*)
+ GUESS=$UNAME_MACHINE-pc-rdos
+ ;;
+ i*86:Fiwix:*:*)
+ GUESS=$UNAME_MACHINE-pc-fiwix
+ ;;
+ *:AROS:*:*)
+ GUESS=$UNAME_MACHINE-unknown-aros
+ ;;
+ x86_64:VMkernel:*:*)
+ GUESS=$UNAME_MACHINE-unknown-esx
+ ;;
+ amd64:Isilon\ OneFS:*:*)
+ GUESS=x86_64-unknown-onefs
+ ;;
+ *:Unleashed:*:*)
+ GUESS=$UNAME_MACHINE-unknown-unleashed$UNAME_RELEASE
+ ;;
+esac
+
+# Do we have a guess based on uname results?
+if test "x$GUESS" != x; then
+ echo "$GUESS"
+ exit
+fi
+
+# No uname command or uname output not recognized.
+set_cc_for_build
+cat > "$dummy.c" <<EOF
+#ifdef _SEQUENT_
+#include <sys/types.h>
+#include <sys/utsname.h>
+#endif
+#if defined(ultrix) || defined(_ultrix) || defined(__ultrix) || defined(__ultrix__)
+#if defined (vax) || defined (__vax) || defined (__vax__) || defined(mips) || defined(__mips) || defined(__mips__) || defined(MIPS) || defined(__MIPS__)
+#include <signal.h>
+#if defined(_SIZE_T_) || defined(SIGLOST)
+#include <sys/utsname.h>
+#endif
+#endif
+#endif
+main ()
+{
+#if defined (sony)
+#if defined (MIPSEB)
+ /* BFD wants "bsd" instead of "newsos". Perhaps BFD should be changed,
+ I don't know.... */
+ printf ("mips-sony-bsd\n"); exit (0);
+#else
+#include <sys/param.h>
+ printf ("m68k-sony-newsos%s\n",
+#ifdef NEWSOS4
+ "4"
+#else
+ ""
+#endif
+ ); exit (0);
+#endif
+#endif
+
+#if defined (NeXT)
+#if !defined (__ARCHITECTURE__)
+#define __ARCHITECTURE__ "m68k"
+#endif
+ int version;
+ version=`(hostinfo | sed -n 's/.*NeXT Mach \([0-9]*\).*/\1/p') 2>/dev/null`;
+ if (version < 4)
+ printf ("%s-next-nextstep%d\n", __ARCHITECTURE__, version);
+ else
+ printf ("%s-next-openstep%d\n", __ARCHITECTURE__, version);
+ exit (0);
+#endif
+
+#if defined (MULTIMAX) || defined (n16)
+#if defined (UMAXV)
+ printf ("ns32k-encore-sysv\n"); exit (0);
+#else
+#if defined (CMU)
+ printf ("ns32k-encore-mach\n"); exit (0);
+#else
+ printf ("ns32k-encore-bsd\n"); exit (0);
+#endif
+#endif
+#endif
+
+#if defined (__386BSD__)
+ printf ("i386-pc-bsd\n"); exit (0);
+#endif
+
+#if defined (sequent)
+#if defined (i386)
+ printf ("i386-sequent-dynix\n"); exit (0);
+#endif
+#if defined (ns32000)
+ printf ("ns32k-sequent-dynix\n"); exit (0);
+#endif
+#endif
+
+#if defined (_SEQUENT_)
+ struct utsname un;
+
+ uname(&un);
+ if (strncmp(un.version, "V2", 2) == 0) {
+ printf ("i386-sequent-ptx2\n"); exit (0);
+ }
+ if (strncmp(un.version, "V1", 2) == 0) { /* XXX is V1 correct? */
+ printf ("i386-sequent-ptx1\n"); exit (0);
+ }
+ printf ("i386-sequent-ptx\n"); exit (0);
+#endif
+
+#if defined (vax)
+#if !defined (ultrix)
+#include <sys/param.h>
+#if defined (BSD)
+#if BSD == 43
+ printf ("vax-dec-bsd4.3\n"); exit (0);
+#else
+#if BSD == 199006
+ printf ("vax-dec-bsd4.3reno\n"); exit (0);
+#else
+ printf ("vax-dec-bsd\n"); exit (0);
+#endif
+#endif
+#else
+ printf ("vax-dec-bsd\n"); exit (0);
+#endif
+#else
+#if defined(_SIZE_T_) || defined(SIGLOST)
+ struct utsname un;
+ uname (&un);
+ printf ("vax-dec-ultrix%s\n", un.release); exit (0);
+#else
+ printf ("vax-dec-ultrix\n"); exit (0);
+#endif
+#endif
+#endif
+#if defined(ultrix) || defined(_ultrix) || defined(__ultrix) || defined(__ultrix__)
+#if defined(mips) || defined(__mips) || defined(__mips__) || defined(MIPS) || defined(__MIPS__)
+#if defined(_SIZE_T_) || defined(SIGLOST)
+ struct utsname *un;
+ uname (&un);
+ printf ("mips-dec-ultrix%s\n", un.release); exit (0);
+#else
+ printf ("mips-dec-ultrix\n"); exit (0);
+#endif
+#endif
+#endif
+
+#if defined (alliant) && defined (i860)
+ printf ("i860-alliant-bsd\n"); exit (0);
+#endif
+
+ exit (1);
+}
+EOF
+
+$CC_FOR_BUILD -o "$dummy" "$dummy.c" 2>/dev/null && SYSTEM_NAME=`"$dummy"` &&
+ { echo "$SYSTEM_NAME"; exit; }
+
+# Apollos put the system type in the environment.
+test -d /usr/apollo && { echo "$ISP-apollo-$SYSTYPE"; exit; }
+
+echo "$0: unable to guess system type" >&2
+
+case $UNAME_MACHINE:$UNAME_SYSTEM in
+ mips:Linux | mips64:Linux)
+ # If we got here on MIPS GNU/Linux, output extra information.
+ cat >&2 <<EOF
+
+NOTE: MIPS GNU/Linux systems require a C compiler to fully recognize
+the system type. Please install a C compiler and try again.
+EOF
+ ;;
+esac
+
+cat >&2 <<EOF
+
+This script (version $timestamp), has failed to recognize the
+operating system you are using. If your script is old, overwrite *all*
+copies of config.guess and config.sub with the latest versions from:
+
+ https://git.savannah.gnu.org/cgit/config.git/plain/config.guess
+and
+ https://git.savannah.gnu.org/cgit/config.git/plain/config.sub
+EOF
+
+our_year=`echo $timestamp | sed 's,-.*,,'`
+thisyear=`date +%Y`
+# shellcheck disable=SC2003
+script_age=`expr "$thisyear" - "$our_year"`
+if test "$script_age" -lt 3 ; then
+ cat >&2 <<EOF
+
+If $0 has already been updated, send the following data and any
+information you think might be pertinent to config-patches at gnu.org to
+provide the necessary information to handle your system.
+
+config.guess timestamp = $timestamp
+
+uname -m = `(uname -m) 2>/dev/null || echo unknown`
+uname -r = `(uname -r) 2>/dev/null || echo unknown`
+uname -s = `(uname -s) 2>/dev/null || echo unknown`
+uname -v = `(uname -v) 2>/dev/null || echo unknown`
+
+/usr/bin/uname -p = `(/usr/bin/uname -p) 2>/dev/null`
+/bin/uname -X = `(/bin/uname -X) 2>/dev/null`
+
+hostinfo = `(hostinfo) 2>/dev/null`
+/bin/universe = `(/bin/universe) 2>/dev/null`
+/usr/bin/arch -k = `(/usr/bin/arch -k) 2>/dev/null`
+/bin/arch = `(/bin/arch) 2>/dev/null`
+/usr/bin/oslevel = `(/usr/bin/oslevel) 2>/dev/null`
+/usr/convex/getsysinfo = `(/usr/convex/getsysinfo) 2>/dev/null`
+
+UNAME_MACHINE = "$UNAME_MACHINE"
+UNAME_RELEASE = "$UNAME_RELEASE"
+UNAME_SYSTEM = "$UNAME_SYSTEM"
+UNAME_VERSION = "$UNAME_VERSION"
+EOF
+fi
+
+exit 1
+
+# Local variables:
+# eval: (add-hook 'before-save-hook 'time-stamp)
+# time-stamp-start: "timestamp='"
+# time-stamp-format: "%:y-%02m-%02d"
+# time-stamp-end: "'"
+# End:
=====================================
config/config.sub
=====================================
@@ -0,0 +1,1890 @@
+#! /bin/sh
+# Configuration validation subroutine script.
+# Copyright 1992-2022 Free Software Foundation, Inc.
+
+# shellcheck disable=SC2006,SC2268 # see below for rationale
+
+timestamp='2022-01-03'
+
+# This file is free software; you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, see <https://www.gnu.org/licenses/>.
+#
+# As a special exception to the GNU General Public License, if you
+# distribute this file as part of a program that contains a
+# configuration script generated by Autoconf, you may include it under
+# the same distribution terms that you use for the rest of that
+# program. This Exception is an additional permission under section 7
+# of the GNU General Public License, version 3 ("GPLv3").
+
+
+# Please send patches to <config-patches at gnu.org>.
+#
+# Configuration subroutine to validate and canonicalize a configuration type.
+# Supply the specified configuration type as an argument.
+# If it is invalid, we print an error message on stderr and exit with code 1.
+# Otherwise, we print the canonical config type on stdout and succeed.
+
+# You can get the latest version of this script from:
+# https://git.savannah.gnu.org/cgit/config.git/plain/config.sub
+
+# This file is supposed to be the same for all GNU packages
+# and recognize all the CPU types, system types and aliases
+# that are meaningful with *any* GNU software.
+# Each package is responsible for reporting which valid configurations
+# it does not support. The user should be able to distinguish
+# a failure to support a valid configuration from a meaningless
+# configuration.
+
+# The goal of this file is to map all the various variations of a given
+# machine specification into a single specification in the form:
+# CPU_TYPE-MANUFACTURER-OPERATING_SYSTEM
+# or in some cases, the newer four-part form:
+# CPU_TYPE-MANUFACTURER-KERNEL-OPERATING_SYSTEM
+# It is wrong to echo any other type of specification.
+
+# The "shellcheck disable" line above the timestamp inhibits complaints
+# about features and limitations of the classic Bourne shell that were
+# superseded or lifted in POSIX. However, this script identifies a wide
+# variety of pre-POSIX systems that do not have POSIX shells at all, and
+# even some reasonably current systems (Solaris 10 as case-in-point) still
+# have a pre-POSIX /bin/sh.
+
+me=`echo "$0" | sed -e 's,.*/,,'`
+
+usage="\
+Usage: $0 [OPTION] CPU-MFR-OPSYS or ALIAS
+
+Canonicalize a configuration name.
+
+Options:
+ -h, --help print this help, then exit
+ -t, --time-stamp print date of last modification, then exit
+ -v, --version print version number, then exit
+
+Report bugs and patches to <config-patches at gnu.org>."
+
+version="\
+GNU config.sub ($timestamp)
+
+Copyright 1992-2022 Free Software Foundation, Inc.
+
+This is free software; see the source for copying conditions. There is NO
+warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE."
+
+help="
+Try \`$me --help' for more information."
+
+# Parse command line
+while test $# -gt 0 ; do
+ case $1 in
+ --time-stamp | --time* | -t )
+ echo "$timestamp" ; exit ;;
+ --version | -v )
+ echo "$version" ; exit ;;
+ --help | --h* | -h )
+ echo "$usage"; exit ;;
+ -- ) # Stop option processing
+ shift; break ;;
+ - ) # Use stdin as input.
+ break ;;
+ -* )
+ echo "$me: invalid option $1$help" >&2
+ exit 1 ;;
+
+ *local*)
+ # First pass through any local machine types.
+ echo "$1"
+ exit ;;
+
+ * )
+ break ;;
+ esac
+done
+
+case $# in
+ 0) echo "$me: missing argument$help" >&2
+ exit 1;;
+ 1) ;;
+ *) echo "$me: too many arguments$help" >&2
+ exit 1;;
+esac
+
+# Split fields of configuration type
+# shellcheck disable=SC2162
+saved_IFS=$IFS
+IFS="-" read field1 field2 field3 field4 <<EOF
+$1
+EOF
+IFS=$saved_IFS
+
+# Separate into logical components for further validation
+case $1 in
+ *-*-*-*-*)
+ echo Invalid configuration \`"$1"\': more than four components >&2
+ exit 1
+ ;;
+ *-*-*-*)
+ basic_machine=$field1-$field2
+ basic_os=$field3-$field4
+ ;;
+ *-*-*)
+ # Ambiguous whether COMPANY is present, or skipped and KERNEL-OS is two
+ # parts
+ maybe_os=$field2-$field3
+ case $maybe_os in
+ nto-qnx* | linux-* | uclinux-uclibc* \
+ | uclinux-gnu* | kfreebsd*-gnu* | knetbsd*-gnu* | netbsd*-gnu* \
+ | netbsd*-eabi* | kopensolaris*-gnu* | cloudabi*-eabi* \
+ | storm-chaos* | os2-emx* | rtmk-nova*)
+ basic_machine=$field1
+ basic_os=$maybe_os
+ ;;
+ android-linux)
+ basic_machine=$field1-unknown
+ basic_os=linux-android
+ ;;
+ *)
+ basic_machine=$field1-$field2
+ basic_os=$field3
+ ;;
+ esac
+ ;;
+ *-*)
+ # A lone config we happen to match not fitting any pattern
+ case $field1-$field2 in
+ decstation-3100)
+ basic_machine=mips-dec
+ basic_os=
+ ;;
+ *-*)
+ # Second component is usually, but not always the OS
+ case $field2 in
+ # Prevent following clause from handling this valid os
+ sun*os*)
+ basic_machine=$field1
+ basic_os=$field2
+ ;;
+ zephyr*)
+ basic_machine=$field1-unknown
+ basic_os=$field2
+ ;;
+ # Manufacturers
+ dec* | mips* | sequent* | encore* | pc533* | sgi* | sony* \
+ | att* | 7300* | 3300* | delta* | motorola* | sun[234]* \
+ | unicom* | ibm* | next | hp | isi* | apollo | altos* \
+ | convergent* | ncr* | news | 32* | 3600* | 3100* \
+ | hitachi* | c[123]* | convex* | sun | crds | omron* | dg \
+ | ultra | tti* | harris | dolphin | highlevel | gould \
+ | cbm | ns | masscomp | apple | axis | knuth | cray \
+ | microblaze* | sim | cisco \
+ | oki | wec | wrs | winbond)
+ basic_machine=$field1-$field2
+ basic_os=
+ ;;
+ *)
+ basic_machine=$field1
+ basic_os=$field2
+ ;;
+ esac
+ ;;
+ esac
+ ;;
+ *)
+ # Convert single-component short-hands not valid as part of
+ # multi-component configurations.
+ case $field1 in
+ 386bsd)
+ basic_machine=i386-pc
+ basic_os=bsd
+ ;;
+ a29khif)
+ basic_machine=a29k-amd
+ basic_os=udi
+ ;;
+ adobe68k)
+ basic_machine=m68010-adobe
+ basic_os=scout
+ ;;
+ alliant)
+ basic_machine=fx80-alliant
+ basic_os=
+ ;;
+ altos | altos3068)
+ basic_machine=m68k-altos
+ basic_os=
+ ;;
+ am29k)
+ basic_machine=a29k-none
+ basic_os=bsd
+ ;;
+ amdahl)
+ basic_machine=580-amdahl
+ basic_os=sysv
+ ;;
+ amiga)
+ basic_machine=m68k-unknown
+ basic_os=
+ ;;
+ amigaos | amigados)
+ basic_machine=m68k-unknown
+ basic_os=amigaos
+ ;;
+ amigaunix | amix)
+ basic_machine=m68k-unknown
+ basic_os=sysv4
+ ;;
+ apollo68)
+ basic_machine=m68k-apollo
+ basic_os=sysv
+ ;;
+ apollo68bsd)
+ basic_machine=m68k-apollo
+ basic_os=bsd
+ ;;
+ aros)
+ basic_machine=i386-pc
+ basic_os=aros
+ ;;
+ aux)
+ basic_machine=m68k-apple
+ basic_os=aux
+ ;;
+ balance)
+ basic_machine=ns32k-sequent
+ basic_os=dynix
+ ;;
+ blackfin)
+ basic_machine=bfin-unknown
+ basic_os=linux
+ ;;
+ cegcc)
+ basic_machine=arm-unknown
+ basic_os=cegcc
+ ;;
+ convex-c1)
+ basic_machine=c1-convex
+ basic_os=bsd
+ ;;
+ convex-c2)
+ basic_machine=c2-convex
+ basic_os=bsd
+ ;;
+ convex-c32)
+ basic_machine=c32-convex
+ basic_os=bsd
+ ;;
+ convex-c34)
+ basic_machine=c34-convex
+ basic_os=bsd
+ ;;
+ convex-c38)
+ basic_machine=c38-convex
+ basic_os=bsd
+ ;;
+ cray)
+ basic_machine=j90-cray
+ basic_os=unicos
+ ;;
+ crds | unos)
+ basic_machine=m68k-crds
+ basic_os=
+ ;;
+ da30)
+ basic_machine=m68k-da30
+ basic_os=
+ ;;
+ decstation | pmax | pmin | dec3100 | decstatn)
+ basic_machine=mips-dec
+ basic_os=
+ ;;
+ delta88)
+ basic_machine=m88k-motorola
+ basic_os=sysv3
+ ;;
+ dicos)
+ basic_machine=i686-pc
+ basic_os=dicos
+ ;;
+ djgpp)
+ basic_machine=i586-pc
+ basic_os=msdosdjgpp
+ ;;
+ ebmon29k)
+ basic_machine=a29k-amd
+ basic_os=ebmon
+ ;;
+ es1800 | OSE68k | ose68k | ose | OSE)
+ basic_machine=m68k-ericsson
+ basic_os=ose
+ ;;
+ gmicro)
+ basic_machine=tron-gmicro
+ basic_os=sysv
+ ;;
+ go32)
+ basic_machine=i386-pc
+ basic_os=go32
+ ;;
+ h8300hms)
+ basic_machine=h8300-hitachi
+ basic_os=hms
+ ;;
+ h8300xray)
+ basic_machine=h8300-hitachi
+ basic_os=xray
+ ;;
+ h8500hms)
+ basic_machine=h8500-hitachi
+ basic_os=hms
+ ;;
+ harris)
+ basic_machine=m88k-harris
+ basic_os=sysv3
+ ;;
+ hp300 | hp300hpux)
+ basic_machine=m68k-hp
+ basic_os=hpux
+ ;;
+ hp300bsd)
+ basic_machine=m68k-hp
+ basic_os=bsd
+ ;;
+ hppaosf)
+ basic_machine=hppa1.1-hp
+ basic_os=osf
+ ;;
+ hppro)
+ basic_machine=hppa1.1-hp
+ basic_os=proelf
+ ;;
+ i386mach)
+ basic_machine=i386-mach
+ basic_os=mach
+ ;;
+ isi68 | isi)
+ basic_machine=m68k-isi
+ basic_os=sysv
+ ;;
+ m68knommu)
+ basic_machine=m68k-unknown
+ basic_os=linux
+ ;;
+ magnum | m3230)
+ basic_machine=mips-mips
+ basic_os=sysv
+ ;;
+ merlin)
+ basic_machine=ns32k-utek
+ basic_os=sysv
+ ;;
+ mingw64)
+ basic_machine=x86_64-pc
+ basic_os=mingw64
+ ;;
+ mingw32)
+ basic_machine=i686-pc
+ basic_os=mingw32
+ ;;
+ mingw32ce)
+ basic_machine=arm-unknown
+ basic_os=mingw32ce
+ ;;
+ monitor)
+ basic_machine=m68k-rom68k
+ basic_os=coff
+ ;;
+ morphos)
+ basic_machine=powerpc-unknown
+ basic_os=morphos
+ ;;
+ moxiebox)
+ basic_machine=moxie-unknown
+ basic_os=moxiebox
+ ;;
+ msdos)
+ basic_machine=i386-pc
+ basic_os=msdos
+ ;;
+ msys)
+ basic_machine=i686-pc
+ basic_os=msys
+ ;;
+ mvs)
+ basic_machine=i370-ibm
+ basic_os=mvs
+ ;;
+ nacl)
+ basic_machine=le32-unknown
+ basic_os=nacl
+ ;;
+ ncr3000)
+ basic_machine=i486-ncr
+ basic_os=sysv4
+ ;;
+ netbsd386)
+ basic_machine=i386-pc
+ basic_os=netbsd
+ ;;
+ netwinder)
+ basic_machine=armv4l-rebel
+ basic_os=linux
+ ;;
+ news | news700 | news800 | news900)
+ basic_machine=m68k-sony
+ basic_os=newsos
+ ;;
+ news1000)
+ basic_machine=m68030-sony
+ basic_os=newsos
+ ;;
+ necv70)
+ basic_machine=v70-nec
+ basic_os=sysv
+ ;;
+ nh3000)
+ basic_machine=m68k-harris
+ basic_os=cxux
+ ;;
+ nh[45]000)
+ basic_machine=m88k-harris
+ basic_os=cxux
+ ;;
+ nindy960)
+ basic_machine=i960-intel
+ basic_os=nindy
+ ;;
+ mon960)
+ basic_machine=i960-intel
+ basic_os=mon960
+ ;;
+ nonstopux)
+ basic_machine=mips-compaq
+ basic_os=nonstopux
+ ;;
+ os400)
+ basic_machine=powerpc-ibm
+ basic_os=os400
+ ;;
+ OSE68000 | ose68000)
+ basic_machine=m68000-ericsson
+ basic_os=ose
+ ;;
+ os68k)
+ basic_machine=m68k-none
+ basic_os=os68k
+ ;;
+ paragon)
+ basic_machine=i860-intel
+ basic_os=osf
+ ;;
+ parisc)
+ basic_machine=hppa-unknown
+ basic_os=linux
+ ;;
+ psp)
+ basic_machine=mipsallegrexel-sony
+ basic_os=psp
+ ;;
+ pw32)
+ basic_machine=i586-unknown
+ basic_os=pw32
+ ;;
+ rdos | rdos64)
+ basic_machine=x86_64-pc
+ basic_os=rdos
+ ;;
+ rdos32)
+ basic_machine=i386-pc
+ basic_os=rdos
+ ;;
+ rom68k)
+ basic_machine=m68k-rom68k
+ basic_os=coff
+ ;;
+ sa29200)
+ basic_machine=a29k-amd
+ basic_os=udi
+ ;;
+ sei)
+ basic_machine=mips-sei
+ basic_os=seiux
+ ;;
+ sequent)
+ basic_machine=i386-sequent
+ basic_os=
+ ;;
+ sps7)
+ basic_machine=m68k-bull
+ basic_os=sysv2
+ ;;
+ st2000)
+ basic_machine=m68k-tandem
+ basic_os=
+ ;;
+ stratus)
+ basic_machine=i860-stratus
+ basic_os=sysv4
+ ;;
+ sun2)
+ basic_machine=m68000-sun
+ basic_os=
+ ;;
+ sun2os3)
+ basic_machine=m68000-sun
+ basic_os=sunos3
+ ;;
+ sun2os4)
+ basic_machine=m68000-sun
+ basic_os=sunos4
+ ;;
+ sun3)
+ basic_machine=m68k-sun
+ basic_os=
+ ;;
+ sun3os3)
+ basic_machine=m68k-sun
+ basic_os=sunos3
+ ;;
+ sun3os4)
+ basic_machine=m68k-sun
+ basic_os=sunos4
+ ;;
+ sun4)
+ basic_machine=sparc-sun
+ basic_os=
+ ;;
+ sun4os3)
+ basic_machine=sparc-sun
+ basic_os=sunos3
+ ;;
+ sun4os4)
+ basic_machine=sparc-sun
+ basic_os=sunos4
+ ;;
+ sun4sol2)
+ basic_machine=sparc-sun
+ basic_os=solaris2
+ ;;
+ sun386 | sun386i | roadrunner)
+ basic_machine=i386-sun
+ basic_os=
+ ;;
+ sv1)
+ basic_machine=sv1-cray
+ basic_os=unicos
+ ;;
+ symmetry)
+ basic_machine=i386-sequent
+ basic_os=dynix
+ ;;
+ t3e)
+ basic_machine=alphaev5-cray
+ basic_os=unicos
+ ;;
+ t90)
+ basic_machine=t90-cray
+ basic_os=unicos
+ ;;
+ toad1)
+ basic_machine=pdp10-xkl
+ basic_os=tops20
+ ;;
+ tpf)
+ basic_machine=s390x-ibm
+ basic_os=tpf
+ ;;
+ udi29k)
+ basic_machine=a29k-amd
+ basic_os=udi
+ ;;
+ ultra3)
+ basic_machine=a29k-nyu
+ basic_os=sym1
+ ;;
+ v810 | necv810)
+ basic_machine=v810-nec
+ basic_os=none
+ ;;
+ vaxv)
+ basic_machine=vax-dec
+ basic_os=sysv
+ ;;
+ vms)
+ basic_machine=vax-dec
+ basic_os=vms
+ ;;
+ vsta)
+ basic_machine=i386-pc
+ basic_os=vsta
+ ;;
+ vxworks960)
+ basic_machine=i960-wrs
+ basic_os=vxworks
+ ;;
+ vxworks68)
+ basic_machine=m68k-wrs
+ basic_os=vxworks
+ ;;
+ vxworks29k)
+ basic_machine=a29k-wrs
+ basic_os=vxworks
+ ;;
+ xbox)
+ basic_machine=i686-pc
+ basic_os=mingw32
+ ;;
+ ymp)
+ basic_machine=ymp-cray
+ basic_os=unicos
+ ;;
+ *)
+ basic_machine=$1
+ basic_os=
+ ;;
+ esac
+ ;;
+esac
+
+# Decode 1-component or ad-hoc basic machines
+case $basic_machine in
+ # Here we handle the default manufacturer of certain CPU types. It is in
+ # some cases the only manufacturer, in others, it is the most popular.
+ w89k)
+ cpu=hppa1.1
+ vendor=winbond
+ ;;
+ op50n)
+ cpu=hppa1.1
+ vendor=oki
+ ;;
+ op60c)
+ cpu=hppa1.1
+ vendor=oki
+ ;;
+ ibm*)
+ cpu=i370
+ vendor=ibm
+ ;;
+ orion105)
+ cpu=clipper
+ vendor=highlevel
+ ;;
+ mac | mpw | mac-mpw)
+ cpu=m68k
+ vendor=apple
+ ;;
+ pmac | pmac-mpw)
+ cpu=powerpc
+ vendor=apple
+ ;;
+
+ # Recognize the various machine names and aliases which stand
+ # for a CPU type and a company and sometimes even an OS.
+ 3b1 | 7300 | 7300-att | att-7300 | pc7300 | safari | unixpc)
+ cpu=m68000
+ vendor=att
+ ;;
+ 3b*)
+ cpu=we32k
+ vendor=att
+ ;;
+ bluegene*)
+ cpu=powerpc
+ vendor=ibm
+ basic_os=cnk
+ ;;
+ decsystem10* | dec10*)
+ cpu=pdp10
+ vendor=dec
+ basic_os=tops10
+ ;;
+ decsystem20* | dec20*)
+ cpu=pdp10
+ vendor=dec
+ basic_os=tops20
+ ;;
+ delta | 3300 | motorola-3300 | motorola-delta \
+ | 3300-motorola | delta-motorola)
+ cpu=m68k
+ vendor=motorola
+ ;;
+ dpx2*)
+ cpu=m68k
+ vendor=bull
+ basic_os=sysv3
+ ;;
+ encore | umax | mmax)
+ cpu=ns32k
+ vendor=encore
+ ;;
+ elxsi)
+ cpu=elxsi
+ vendor=elxsi
+ basic_os=${basic_os:-bsd}
+ ;;
+ fx2800)
+ cpu=i860
+ vendor=alliant
+ ;;
+ genix)
+ cpu=ns32k
+ vendor=ns
+ ;;
+ h3050r* | hiux*)
+ cpu=hppa1.1
+ vendor=hitachi
+ basic_os=hiuxwe2
+ ;;
+ hp3k9[0-9][0-9] | hp9[0-9][0-9])
+ cpu=hppa1.0
+ vendor=hp
+ ;;
+ hp9k2[0-9][0-9] | hp9k31[0-9])
+ cpu=m68000
+ vendor=hp
+ ;;
+ hp9k3[2-9][0-9])
+ cpu=m68k
+ vendor=hp
+ ;;
+ hp9k6[0-9][0-9] | hp6[0-9][0-9])
+ cpu=hppa1.0
+ vendor=hp
+ ;;
+ hp9k7[0-79][0-9] | hp7[0-79][0-9])
+ cpu=hppa1.1
+ vendor=hp
+ ;;
+ hp9k78[0-9] | hp78[0-9])
+ # FIXME: really hppa2.0-hp
+ cpu=hppa1.1
+ vendor=hp
+ ;;
+ hp9k8[67]1 | hp8[67]1 | hp9k80[24] | hp80[24] | hp9k8[78]9 | hp8[78]9 | hp9k893 | hp893)
+ # FIXME: really hppa2.0-hp
+ cpu=hppa1.1
+ vendor=hp
+ ;;
+ hp9k8[0-9][13679] | hp8[0-9][13679])
+ cpu=hppa1.1
+ vendor=hp
+ ;;
+ hp9k8[0-9][0-9] | hp8[0-9][0-9])
+ cpu=hppa1.0
+ vendor=hp
+ ;;
+ i*86v32)
+ cpu=`echo "$1" | sed -e 's/86.*/86/'`
+ vendor=pc
+ basic_os=sysv32
+ ;;
+ i*86v4*)
+ cpu=`echo "$1" | sed -e 's/86.*/86/'`
+ vendor=pc
+ basic_os=sysv4
+ ;;
+ i*86v)
+ cpu=`echo "$1" | sed -e 's/86.*/86/'`
+ vendor=pc
+ basic_os=sysv
+ ;;
+ i*86sol2)
+ cpu=`echo "$1" | sed -e 's/86.*/86/'`
+ vendor=pc
+ basic_os=solaris2
+ ;;
+ j90 | j90-cray)
+ cpu=j90
+ vendor=cray
+ basic_os=${basic_os:-unicos}
+ ;;
+ iris | iris4d)
+ cpu=mips
+ vendor=sgi
+ case $basic_os in
+ irix*)
+ ;;
+ *)
+ basic_os=irix4
+ ;;
+ esac
+ ;;
+ miniframe)
+ cpu=m68000
+ vendor=convergent
+ ;;
+ *mint | mint[0-9]* | *MiNT | *MiNT[0-9]*)
+ cpu=m68k
+ vendor=atari
+ basic_os=mint
+ ;;
+ news-3600 | risc-news)
+ cpu=mips
+ vendor=sony
+ basic_os=newsos
+ ;;
+ next | m*-next)
+ cpu=m68k
+ vendor=next
+ case $basic_os in
+ openstep*)
+ ;;
+ nextstep*)
+ ;;
+ ns2*)
+ basic_os=nextstep2
+ ;;
+ *)
+ basic_os=nextstep3
+ ;;
+ esac
+ ;;
+ np1)
+ cpu=np1
+ vendor=gould
+ ;;
+ op50n-* | op60c-*)
+ cpu=hppa1.1
+ vendor=oki
+ basic_os=proelf
+ ;;
+ pa-hitachi)
+ cpu=hppa1.1
+ vendor=hitachi
+ basic_os=hiuxwe2
+ ;;
+ pbd)
+ cpu=sparc
+ vendor=tti
+ ;;
+ pbb)
+ cpu=m68k
+ vendor=tti
+ ;;
+ pc532)
+ cpu=ns32k
+ vendor=pc532
+ ;;
+ pn)
+ cpu=pn
+ vendor=gould
+ ;;
+ power)
+ cpu=power
+ vendor=ibm
+ ;;
+ ps2)
+ cpu=i386
+ vendor=ibm
+ ;;
+ rm[46]00)
+ cpu=mips
+ vendor=siemens
+ ;;
+ rtpc | rtpc-*)
+ cpu=romp
+ vendor=ibm
+ ;;
+ sde)
+ cpu=mipsisa32
+ vendor=sde
+ basic_os=${basic_os:-elf}
+ ;;
+ simso-wrs)
+ cpu=sparclite
+ vendor=wrs
+ basic_os=vxworks
+ ;;
+ tower | tower-32)
+ cpu=m68k
+ vendor=ncr
+ ;;
+ vpp*|vx|vx-*)
+ cpu=f301
+ vendor=fujitsu
+ ;;
+ w65)
+ cpu=w65
+ vendor=wdc
+ ;;
+ w89k-*)
+ cpu=hppa1.1
+ vendor=winbond
+ basic_os=proelf
+ ;;
+ none)
+ cpu=none
+ vendor=none
+ ;;
+ leon|leon[3-9])
+ cpu=sparc
+ vendor=$basic_machine
+ ;;
+ leon-*|leon[3-9]-*)
+ cpu=sparc
+ vendor=`echo "$basic_machine" | sed 's/-.*//'`
+ ;;
+
+ *-*)
+ # shellcheck disable=SC2162
+ saved_IFS=$IFS
+ IFS="-" read cpu vendor <<EOF
+$basic_machine
+EOF
+ IFS=$saved_IFS
+ ;;
+ # We use `pc' rather than `unknown'
+ # because (1) that's what they normally are, and
+ # (2) the word "unknown" tends to confuse beginning users.
+ i*86 | x86_64)
+ cpu=$basic_machine
+ vendor=pc
+ ;;
+ # These rules are duplicated from below for sake of the special case above;
+ # i.e. things that normalized to x86 arches should also default to "pc"
+ pc98)
+ cpu=i386
+ vendor=pc
+ ;;
+ x64 | amd64)
+ cpu=x86_64
+ vendor=pc
+ ;;
+ # Recognize the basic CPU types without company name.
+ *)
+ cpu=$basic_machine
+ vendor=unknown
+ ;;
+esac
+
+unset -v basic_machine
+
+# Decode basic machines in the full and proper CPU-Company form.
+case $cpu-$vendor in
+ # Here we handle the default manufacturer of certain CPU types in canonical form. It is in
+ # some cases the only manufacturer, in others, it is the most popular.
+ craynv-unknown)
+ vendor=cray
+ basic_os=${basic_os:-unicosmp}
+ ;;
+ c90-unknown | c90-cray)
+ vendor=cray
+ basic_os=${Basic_os:-unicos}
+ ;;
+ fx80-unknown)
+ vendor=alliant
+ ;;
+ romp-unknown)
+ vendor=ibm
+ ;;
+ mmix-unknown)
+ vendor=knuth
+ ;;
+ microblaze-unknown | microblazeel-unknown)
+ vendor=xilinx
+ ;;
+ rs6000-unknown)
+ vendor=ibm
+ ;;
+ vax-unknown)
+ vendor=dec
+ ;;
+ pdp11-unknown)
+ vendor=dec
+ ;;
+ we32k-unknown)
+ vendor=att
+ ;;
+ cydra-unknown)
+ vendor=cydrome
+ ;;
+ i370-ibm*)
+ vendor=ibm
+ ;;
+ orion-unknown)
+ vendor=highlevel
+ ;;
+ xps-unknown | xps100-unknown)
+ cpu=xps100
+ vendor=honeywell
+ ;;
+
+ # Here we normalize CPU types with a missing or matching vendor
+ armh-unknown | armh-alt)
+ cpu=armv7l
+ vendor=alt
+ basic_os=${basic_os:-linux-gnueabihf}
+ ;;
+ dpx20-unknown | dpx20-bull)
+ cpu=rs6000
+ vendor=bull
+ basic_os=${basic_os:-bosx}
+ ;;
+
+ # Here we normalize CPU types irrespective of the vendor
+ amd64-*)
+ cpu=x86_64
+ ;;
+ blackfin-*)
+ cpu=bfin
+ basic_os=linux
+ ;;
+ c54x-*)
+ cpu=tic54x
+ ;;
+ c55x-*)
+ cpu=tic55x
+ ;;
+ c6x-*)
+ cpu=tic6x
+ ;;
+ e500v[12]-*)
+ cpu=powerpc
+ basic_os=${basic_os}"spe"
+ ;;
+ mips3*-*)
+ cpu=mips64
+ ;;
+ ms1-*)
+ cpu=mt
+ ;;
+ m68knommu-*)
+ cpu=m68k
+ basic_os=linux
+ ;;
+ m9s12z-* | m68hcs12z-* | hcs12z-* | s12z-*)
+ cpu=s12z
+ ;;
+ openrisc-*)
+ cpu=or32
+ ;;
+ parisc-*)
+ cpu=hppa
+ basic_os=linux
+ ;;
+ pentium-* | p5-* | k5-* | k6-* | nexgen-* | viac3-*)
+ cpu=i586
+ ;;
+ pentiumpro-* | p6-* | 6x86-* | athlon-* | athalon_*-*)
+ cpu=i686
+ ;;
+ pentiumii-* | pentium2-* | pentiumiii-* | pentium3-*)
+ cpu=i686
+ ;;
+ pentium4-*)
+ cpu=i786
+ ;;
+ pc98-*)
+ cpu=i386
+ ;;
+ ppc-* | ppcbe-*)
+ cpu=powerpc
+ ;;
+ ppcle-* | powerpclittle-*)
+ cpu=powerpcle
+ ;;
+ ppc64-*)
+ cpu=powerpc64
+ ;;
+ ppc64le-* | powerpc64little-*)
+ cpu=powerpc64le
+ ;;
+ sb1-*)
+ cpu=mipsisa64sb1
+ ;;
+ sb1el-*)
+ cpu=mipsisa64sb1el
+ ;;
+ sh5e[lb]-*)
+ cpu=`echo "$cpu" | sed 's/^\(sh.\)e\(.\)$/\1\2e/'`
+ ;;
+ spur-*)
+ cpu=spur
+ ;;
+ strongarm-* | thumb-*)
+ cpu=arm
+ ;;
+ tx39-*)
+ cpu=mipstx39
+ ;;
+ tx39el-*)
+ cpu=mipstx39el
+ ;;
+ x64-*)
+ cpu=x86_64
+ ;;
+ xscale-* | xscalee[bl]-*)
+ cpu=`echo "$cpu" | sed 's/^xscale/arm/'`
+ ;;
+ arm64-* | aarch64le-*)
+ cpu=aarch64
+ ;;
+
+ # Recognize the canonical CPU Types that limit and/or modify the
+ # company names they are paired with.
+ cr16-*)
+ basic_os=${basic_os:-elf}
+ ;;
+ crisv32-* | etraxfs*-*)
+ cpu=crisv32
+ vendor=axis
+ ;;
+ cris-* | etrax*-*)
+ cpu=cris
+ vendor=axis
+ ;;
+ crx-*)
+ basic_os=${basic_os:-elf}
+ ;;
+ neo-tandem)
+ cpu=neo
+ vendor=tandem
+ ;;
+ nse-tandem)
+ cpu=nse
+ vendor=tandem
+ ;;
+ nsr-tandem)
+ cpu=nsr
+ vendor=tandem
+ ;;
+ nsv-tandem)
+ cpu=nsv
+ vendor=tandem
+ ;;
+ nsx-tandem)
+ cpu=nsx
+ vendor=tandem
+ ;;
+ mipsallegrexel-sony)
+ cpu=mipsallegrexel
+ vendor=sony
+ ;;
+ tile*-*)
+ basic_os=${basic_os:-linux-gnu}
+ ;;
+
+ *)
+ # Recognize the canonical CPU types that are allowed with any
+ # company name.
+ case $cpu in
+ 1750a | 580 \
+ | a29k \
+ | aarch64 | aarch64_be \
+ | abacus \
+ | alpha | alphaev[4-8] | alphaev56 | alphaev6[78] \
+ | alpha64 | alpha64ev[4-8] | alpha64ev56 | alpha64ev6[78] \
+ | alphapca5[67] | alpha64pca5[67] \
+ | am33_2.0 \
+ | amdgcn \
+ | arc | arceb | arc32 | arc64 \
+ | arm | arm[lb]e | arme[lb] | armv* \
+ | avr | avr32 \
+ | asmjs \
+ | ba \
+ | be32 | be64 \
+ | bfin | bpf | bs2000 \
+ | c[123]* | c30 | [cjt]90 | c4x \
+ | c8051 | clipper | craynv | csky | cydra \
+ | d10v | d30v | dlx | dsp16xx \
+ | e2k | elxsi | epiphany \
+ | f30[01] | f700 | fido | fr30 | frv | ft32 | fx80 \
+ | h8300 | h8500 \
+ | hppa | hppa1.[01] | hppa2.0 | hppa2.0[nw] | hppa64 \
+ | hexagon \
+ | i370 | i*86 | i860 | i960 | ia16 | ia64 \
+ | ip2k | iq2000 \
+ | k1om \
+ | le32 | le64 \
+ | lm32 \
+ | loongarch32 | loongarch64 | loongarchx32 \
+ | m32c | m32r | m32rle \
+ | m5200 | m68000 | m680[012346]0 | m68360 | m683?2 | m68k \
+ | m6811 | m68hc11 | m6812 | m68hc12 | m68hcs12x \
+ | m88110 | m88k | maxq | mb | mcore | mep | metag \
+ | microblaze | microblazeel \
+ | mips | mipsbe | mipseb | mipsel | mipsle \
+ | mips16 \
+ | mips64 | mips64eb | mips64el \
+ | mips64octeon | mips64octeonel \
+ | mips64orion | mips64orionel \
+ | mips64r5900 | mips64r5900el \
+ | mips64vr | mips64vrel \
+ | mips64vr4100 | mips64vr4100el \
+ | mips64vr4300 | mips64vr4300el \
+ | mips64vr5000 | mips64vr5000el \
+ | mips64vr5900 | mips64vr5900el \
+ | mipsisa32 | mipsisa32el \
+ | mipsisa32r2 | mipsisa32r2el \
+ | mipsisa32r3 | mipsisa32r3el \
+ | mipsisa32r5 | mipsisa32r5el \
+ | mipsisa32r6 | mipsisa32r6el \
+ | mipsisa64 | mipsisa64el \
+ | mipsisa64r2 | mipsisa64r2el \
+ | mipsisa64r3 | mipsisa64r3el \
+ | mipsisa64r5 | mipsisa64r5el \
+ | mipsisa64r6 | mipsisa64r6el \
+ | mipsisa64sb1 | mipsisa64sb1el \
+ | mipsisa64sr71k | mipsisa64sr71kel \
+ | mipsr5900 | mipsr5900el \
+ | mipstx39 | mipstx39el \
+ | mmix \
+ | mn10200 | mn10300 \
+ | moxie \
+ | mt \
+ | msp430 \
+ | nds32 | nds32le | nds32be \
+ | nfp \
+ | nios | nios2 | nios2eb | nios2el \
+ | none | np1 | ns16k | ns32k | nvptx \
+ | open8 \
+ | or1k* \
+ | or32 \
+ | orion \
+ | picochip \
+ | pdp10 | pdp11 | pj | pjl | pn | power \
+ | powerpc | powerpc64 | powerpc64le | powerpcle | powerpcspe \
+ | pru \
+ | pyramid \
+ | riscv | riscv32 | riscv32be | riscv64 | riscv64be \
+ | rl78 | romp | rs6000 | rx \
+ | s390 | s390x \
+ | score \
+ | sh | shl \
+ | sh[1234] | sh[24]a | sh[24]ae[lb] | sh[23]e | she[lb] | sh[lb]e \
+ | sh[1234]e[lb] | sh[12345][lb]e | sh[23]ele | sh64 | sh64le \
+ | sparc | sparc64 | sparc64b | sparc64v | sparc86x | sparclet \
+ | sparclite \
+ | sparcv8 | sparcv9 | sparcv9b | sparcv9v | sv1 | sx* \
+ | spu \
+ | tahoe \
+ | thumbv7* \
+ | tic30 | tic4x | tic54x | tic55x | tic6x | tic80 \
+ | tron \
+ | ubicom32 \
+ | v70 | v850 | v850e | v850e1 | v850es | v850e2 | v850e2v3 \
+ | vax \
+ | visium \
+ | w65 \
+ | wasm32 | wasm64 \
+ | we32k \
+ | x86 | x86_64 | xc16x | xgate | xps100 \
+ | xstormy16 | xtensa* \
+ | ymp \
+ | z8k | z80)
+ ;;
+
+ *)
+ echo Invalid configuration \`"$1"\': machine \`"$cpu-$vendor"\' not recognized 1>&2
+ exit 1
+ ;;
+ esac
+ ;;
+esac
+
+# Here we canonicalize certain aliases for manufacturers.
+case $vendor in
+ digital*)
+ vendor=dec
+ ;;
+ commodore*)
+ vendor=cbm
+ ;;
+ *)
+ ;;
+esac
+
+# Decode manufacturer-specific aliases for certain operating systems.
+
+if test x$basic_os != x
+then
+
+# First recognize some ad-hoc cases, or perhaps split kernel-os, or else just
+# set os.
+case $basic_os in
+ gnu/linux*)
+ kernel=linux
+ os=`echo "$basic_os" | sed -e 's|gnu/linux|gnu|'`
+ ;;
+ os2-emx)
+ kernel=os2
+ os=`echo "$basic_os" | sed -e 's|os2-emx|emx|'`
+ ;;
+ nto-qnx*)
+ kernel=nto
+ os=`echo "$basic_os" | sed -e 's|nto-qnx|qnx|'`
+ ;;
+ *-*)
+ # shellcheck disable=SC2162
+ saved_IFS=$IFS
+ IFS="-" read kernel os <<EOF
+$basic_os
+EOF
+ IFS=$saved_IFS
+ ;;
+ # Default OS when just kernel was specified
+ nto*)
+ kernel=nto
+ os=`echo "$basic_os" | sed -e 's|nto|qnx|'`
+ ;;
+ linux*)
+ kernel=linux
+ os=`echo "$basic_os" | sed -e 's|linux|gnu|'`
+ ;;
+ *)
+ kernel=
+ os=$basic_os
+ ;;
+esac
+
+# Now, normalize the OS (knowing we just have one component, it's not a kernel,
+# etc.)
+case $os in
+ # First match some system type aliases that might get confused
+ # with valid system types.
+ # solaris* is a basic system type, with this one exception.
+ auroraux)
+ os=auroraux
+ ;;
+ bluegene*)
+ os=cnk
+ ;;
+ solaris1 | solaris1.*)
+ os=`echo "$os" | sed -e 's|solaris1|sunos4|'`
+ ;;
+ solaris)
+ os=solaris2
+ ;;
+ unixware*)
+ os=sysv4.2uw
+ ;;
+ # es1800 is here to avoid being matched by es* (a different OS)
+ es1800*)
+ os=ose
+ ;;
+ # Some version numbers need modification
+ chorusos*)
+ os=chorusos
+ ;;
+ isc)
+ os=isc2.2
+ ;;
+ sco6)
+ os=sco5v6
+ ;;
+ sco5)
+ os=sco3.2v5
+ ;;
+ sco4)
+ os=sco3.2v4
+ ;;
+ sco3.2.[4-9]*)
+ os=`echo "$os" | sed -e 's/sco3.2./sco3.2v/'`
+ ;;
+ sco*v* | scout)
+ # Don't match below
+ ;;
+ sco*)
+ os=sco3.2v2
+ ;;
+ psos*)
+ os=psos
+ ;;
+ qnx*)
+ os=qnx
+ ;;
+ hiux*)
+ os=hiuxwe2
+ ;;
+ lynx*178)
+ os=lynxos178
+ ;;
+ lynx*5)
+ os=lynxos5
+ ;;
+ lynxos*)
+ # don't get caught up in next wildcard
+ ;;
+ lynx*)
+ os=lynxos
+ ;;
+ mac[0-9]*)
+ os=`echo "$os" | sed -e 's|mac|macos|'`
+ ;;
+ opened*)
+ os=openedition
+ ;;
+ os400*)
+ os=os400
+ ;;
+ sunos5*)
+ os=`echo "$os" | sed -e 's|sunos5|solaris2|'`
+ ;;
+ sunos6*)
+ os=`echo "$os" | sed -e 's|sunos6|solaris3|'`
+ ;;
+ wince*)
+ os=wince
+ ;;
+ utek*)
+ os=bsd
+ ;;
+ dynix*)
+ os=bsd
+ ;;
+ acis*)
+ os=aos
+ ;;
+ atheos*)
+ os=atheos
+ ;;
+ syllable*)
+ os=syllable
+ ;;
+ 386bsd)
+ os=bsd
+ ;;
+ ctix* | uts*)
+ os=sysv
+ ;;
+ nova*)
+ os=rtmk-nova
+ ;;
+ ns2)
+ os=nextstep2
+ ;;
+ # Preserve the version number of sinix5.
+ sinix5.*)
+ os=`echo "$os" | sed -e 's|sinix|sysv|'`
+ ;;
+ sinix*)
+ os=sysv4
+ ;;
+ tpf*)
+ os=tpf
+ ;;
+ triton*)
+ os=sysv3
+ ;;
+ oss*)
+ os=sysv3
+ ;;
+ svr4*)
+ os=sysv4
+ ;;
+ svr3)
+ os=sysv3
+ ;;
+ sysvr4)
+ os=sysv4
+ ;;
+ ose*)
+ os=ose
+ ;;
+ *mint | mint[0-9]* | *MiNT | MiNT[0-9]*)
+ os=mint
+ ;;
+ dicos*)
+ os=dicos
+ ;;
+ pikeos*)
+ # Until real need of OS specific support for
+ # particular features comes up, bare metal
+ # configurations are quite functional.
+ case $cpu in
+ arm*)
+ os=eabi
+ ;;
+ *)
+ os=elf
+ ;;
+ esac
+ ;;
+ *)
+ # No normalization, but not necessarily accepted, that comes below.
+ ;;
+esac
+
+else
+
+# Here we handle the default operating systems that come with various machines.
+# The value should be what the vendor currently ships out the door with their
+# machine or put another way, the most popular os provided with the machine.
+
+# Note that if you're going to try to match "-MANUFACTURER" here (say,
+# "-sun"), then you have to tell the case statement up towards the top
+# that MANUFACTURER isn't an operating system. Otherwise, code above
+# will signal an error saying that MANUFACTURER isn't an operating
+# system, and we'll never get to this point.
+
+kernel=
+case $cpu-$vendor in
+ score-*)
+ os=elf
+ ;;
+ spu-*)
+ os=elf
+ ;;
+ *-acorn)
+ os=riscix1.2
+ ;;
+ arm*-rebel)
+ kernel=linux
+ os=gnu
+ ;;
+ arm*-semi)
+ os=aout
+ ;;
+ c4x-* | tic4x-*)
+ os=coff
+ ;;
+ c8051-*)
+ os=elf
+ ;;
+ clipper-intergraph)
+ os=clix
+ ;;
+ hexagon-*)
+ os=elf
+ ;;
+ tic54x-*)
+ os=coff
+ ;;
+ tic55x-*)
+ os=coff
+ ;;
+ tic6x-*)
+ os=coff
+ ;;
+ # This must come before the *-dec entry.
+ pdp10-*)
+ os=tops20
+ ;;
+ pdp11-*)
+ os=none
+ ;;
+ *-dec | vax-*)
+ os=ultrix4.2
+ ;;
+ m68*-apollo)
+ os=domain
+ ;;
+ i386-sun)
+ os=sunos4.0.2
+ ;;
+ m68000-sun)
+ os=sunos3
+ ;;
+ m68*-cisco)
+ os=aout
+ ;;
+ mep-*)
+ os=elf
+ ;;
+ mips*-cisco)
+ os=elf
+ ;;
+ mips*-*)
+ os=elf
+ ;;
+ or32-*)
+ os=coff
+ ;;
+ *-tti) # must be before sparc entry or we get the wrong os.
+ os=sysv3
+ ;;
+ sparc-* | *-sun)
+ os=sunos4.1.1
+ ;;
+ pru-*)
+ os=elf
+ ;;
+ *-be)
+ os=beos
+ ;;
+ *-ibm)
+ os=aix
+ ;;
+ *-knuth)
+ os=mmixware
+ ;;
+ *-wec)
+ os=proelf
+ ;;
+ *-winbond)
+ os=proelf
+ ;;
+ *-oki)
+ os=proelf
+ ;;
+ *-hp)
+ os=hpux
+ ;;
+ *-hitachi)
+ os=hiux
+ ;;
+ i860-* | *-att | *-ncr | *-altos | *-motorola | *-convergent)
+ os=sysv
+ ;;
+ *-cbm)
+ os=amigaos
+ ;;
+ *-dg)
+ os=dgux
+ ;;
+ *-dolphin)
+ os=sysv3
+ ;;
+ m68k-ccur)
+ os=rtu
+ ;;
+ m88k-omron*)
+ os=luna
+ ;;
+ *-next)
+ os=nextstep
+ ;;
+ *-sequent)
+ os=ptx
+ ;;
+ *-crds)
+ os=unos
+ ;;
+ *-ns)
+ os=genix
+ ;;
+ i370-*)
+ os=mvs
+ ;;
+ *-gould)
+ os=sysv
+ ;;
+ *-highlevel)
+ os=bsd
+ ;;
+ *-encore)
+ os=bsd
+ ;;
+ *-sgi)
+ os=irix
+ ;;
+ *-siemens)
+ os=sysv4
+ ;;
+ *-masscomp)
+ os=rtu
+ ;;
+ f30[01]-fujitsu | f700-fujitsu)
+ os=uxpv
+ ;;
+ *-rom68k)
+ os=coff
+ ;;
+ *-*bug)
+ os=coff
+ ;;
+ *-apple)
+ os=macos
+ ;;
+ *-atari*)
+ os=mint
+ ;;
+ *-wrs)
+ os=vxworks
+ ;;
+ *)
+ os=none
+ ;;
+esac
+
+fi
+
+# Now, validate our (potentially fixed-up) OS.
+case $os in
+ # Sometimes we do "kernel-libc", so those need to count as OSes.
+ musl* | newlib* | relibc* | uclibc*)
+ ;;
+ # Likewise for "kernel-abi"
+ eabi* | gnueabi*)
+ ;;
+ # VxWorks passes extra cpu info in the 4th filed.
+ simlinux | simwindows | spe)
+ ;;
+ # Now accept the basic system types.
+ # The portable systems comes first.
+ # Each alternative MUST end in a * to match a version number.
+ gnu* | android* | bsd* | mach* | minix* | genix* | ultrix* | irix* \
+ | *vms* | esix* | aix* | cnk* | sunos | sunos[34]* \
+ | hpux* | unos* | osf* | luna* | dgux* | auroraux* | solaris* \
+ | sym* | plan9* | psp* | sim* | xray* | os68k* | v88r* \
+ | hiux* | abug | nacl* | netware* | windows* \
+ | os9* | macos* | osx* | ios* \
+ | mpw* | magic* | mmixware* | mon960* | lnews* \
+ | amigaos* | amigados* | msdos* | newsos* | unicos* | aof* \
+ | aos* | aros* | cloudabi* | sortix* | twizzler* \
+ | nindy* | vxsim* | vxworks* | ebmon* | hms* | mvs* \
+ | clix* | riscos* | uniplus* | iris* | isc* | rtu* | xenix* \
+ | mirbsd* | netbsd* | dicos* | openedition* | ose* \
+ | bitrig* | openbsd* | secbsd* | solidbsd* | libertybsd* | os108* \
+ | ekkobsd* | freebsd* | riscix* | lynxos* | os400* \
+ | bosx* | nextstep* | cxux* | aout* | elf* | oabi* \
+ | ptx* | coff* | ecoff* | winnt* | domain* | vsta* \
+ | udi* | lites* | ieee* | go32* | aux* | hcos* \
+ | chorusrdb* | cegcc* | glidix* | serenity* \
+ | cygwin* | msys* | pe* | moss* | proelf* | rtems* \
+ | midipix* | mingw32* | mingw64* | mint* \
+ | uxpv* | beos* | mpeix* | udk* | moxiebox* \
+ | interix* | uwin* | mks* | rhapsody* | darwin* \
+ | openstep* | oskit* | conix* | pw32* | nonstopux* \
+ | storm-chaos* | tops10* | tenex* | tops20* | its* \
+ | os2* | vos* | palmos* | uclinux* | nucleus* | morphos* \
+ | scout* | superux* | sysv* | rtmk* | tpf* | windiss* \
+ | powermax* | dnix* | nx6 | nx7 | sei* | dragonfly* \
+ | skyos* | haiku* | rdos* | toppers* | drops* | es* \
+ | onefs* | tirtos* | phoenix* | fuchsia* | redox* | bme* \
+ | midnightbsd* | amdhsa* | unleashed* | emscripten* | wasi* \
+ | nsk* | powerunix* | genode* | zvmoe* | qnx* | emx* | zephyr* \
+ | fiwix* )
+ ;;
+ # This one is extra strict with allowed versions
+ sco3.2v2 | sco3.2v[4-9]* | sco5v6*)
+ # Don't forget version if it is 3.2v4 or newer.
+ ;;
+ none)
+ ;;
+ *)
+ echo Invalid configuration \`"$1"\': OS \`"$os"\' not recognized 1>&2
+ exit 1
+ ;;
+esac
+
+# As a final step for OS-related things, validate the OS-kernel combination
+# (given a valid OS), if there is a kernel.
+case $kernel-$os in
+ linux-gnu* | linux-dietlibc* | linux-android* | linux-newlib* \
+ | linux-musl* | linux-relibc* | linux-uclibc* )
+ ;;
+ uclinux-uclibc* )
+ ;;
+ -dietlibc* | -newlib* | -musl* | -relibc* | -uclibc* )
+ # These are just libc implementations, not actual OSes, and thus
+ # require a kernel.
+ echo "Invalid configuration \`$1': libc \`$os' needs explicit kernel." 1>&2
+ exit 1
+ ;;
+ kfreebsd*-gnu* | kopensolaris*-gnu*)
+ ;;
+ vxworks-simlinux | vxworks-simwindows | vxworks-spe)
+ ;;
+ nto-qnx*)
+ ;;
+ os2-emx)
+ ;;
+ *-eabi* | *-gnueabi*)
+ ;;
+ -*)
+ # Blank kernel with real OS is always fine.
+ ;;
+ *-*)
+ echo "Invalid configuration \`$1': Kernel \`$kernel' not known to work with OS \`$os'." 1>&2
+ exit 1
+ ;;
+esac
+
+# Here we handle the case where we know the os, and the CPU type, but not the
+# manufacturer. We pick the logical manufacturer.
+case $vendor in
+ unknown)
+ case $cpu-$os in
+ *-riscix*)
+ vendor=acorn
+ ;;
+ *-sunos*)
+ vendor=sun
+ ;;
+ *-cnk* | *-aix*)
+ vendor=ibm
+ ;;
+ *-beos*)
+ vendor=be
+ ;;
+ *-hpux*)
+ vendor=hp
+ ;;
+ *-mpeix*)
+ vendor=hp
+ ;;
+ *-hiux*)
+ vendor=hitachi
+ ;;
+ *-unos*)
+ vendor=crds
+ ;;
+ *-dgux*)
+ vendor=dg
+ ;;
+ *-luna*)
+ vendor=omron
+ ;;
+ *-genix*)
+ vendor=ns
+ ;;
+ *-clix*)
+ vendor=intergraph
+ ;;
+ *-mvs* | *-opened*)
+ vendor=ibm
+ ;;
+ *-os400*)
+ vendor=ibm
+ ;;
+ s390-* | s390x-*)
+ vendor=ibm
+ ;;
+ *-ptx*)
+ vendor=sequent
+ ;;
+ *-tpf*)
+ vendor=ibm
+ ;;
+ *-vxsim* | *-vxworks* | *-windiss*)
+ vendor=wrs
+ ;;
+ *-aux*)
+ vendor=apple
+ ;;
+ *-hms*)
+ vendor=hitachi
+ ;;
+ *-mpw* | *-macos*)
+ vendor=apple
+ ;;
+ *-*mint | *-mint[0-9]* | *-*MiNT | *-MiNT[0-9]*)
+ vendor=atari
+ ;;
+ *-vos*)
+ vendor=stratus
+ ;;
+ esac
+ ;;
+esac
+
+echo "$cpu-$vendor-${kernel:+$kernel-}$os"
+exit
+
+# Local variables:
+# eval: (add-hook 'before-save-hook 'time-stamp)
+# time-stamp-start: "timestamp='"
+# time-stamp-format: "%:y-%02m-%02d"
+# time-stamp-end: "'"
+# End:
=====================================
configure.ac
=====================================
@@ -2,7 +2,7 @@
# Process this file with autoconf to produce a configure script.
AC_PREREQ(2.59)
-AC_INIT([Stacks], [2.67])
+AC_INIT([Stacks], [2.68])
AC_CONFIG_AUX_DIR([config])
AM_INIT_AUTOMAKE([-Wall -Werror foreign parallel-tests subdir-objects])
AC_CONFIG_SRCDIR([src/ustacks.cc])
=====================================
scripts/denovo_map.pl
=====================================
@@ -1,6 +1,6 @@
#!/usr/bin/env perl
#
-# Copyright 2010-2023, Julian Catchen <jcatchen at illinois.edu>
+# Copyright 2010-2024, Julian Catchen <jcatchen at illinois.edu>
#
# This file is part of Stacks.
#
@@ -540,8 +540,10 @@ sub parse_population_map {
while ($line = <$fh>) {
chomp $line;
+
next if ($line =~ /^\s*#/);
-
+ next if (length($line) == 0);
+
@parts = split(/\t/, $line);
if (scalar(@parts) != 2 and scalar(@parts) != 3) {
die("Unable to parse population map, '$popmap_path' (expected 2 or 3 columns, found " . scalar(@parts) . "); at line:\n$line\n");
=====================================
scripts/ref_map.pl
=====================================
@@ -1,6 +1,6 @@
#!/usr/bin/env perl
#
-# Copyright 2010-2021, Julian Catchen <jcatchen at illinois.edu>
+# Copyright 2010-2024, Julian Catchen <jcatchen at illinois.edu>
#
# This file is part of Stacks.
#
@@ -165,6 +165,7 @@ sub parse_population_map {
chomp $line;
next if ($line =~ /^\s*#/);
+ next if (length($line) == 0);
@parts = split(/\t/, $line);
if (scalar(@parts) != 2 and scalar(@parts) != 3) {
=====================================
src/PopMap.h
=====================================
@@ -1,6 +1,6 @@
// -*-mode:c++; c-style:k&r; c-basic-offset:4;-*-
//
-// Copyright 2011-2016, Julian Catchen <jcatchen at illinois.edu>
+// Copyright 2011-2024, Julian Catchen <jcatchen at illinois.edu>
//
// This file is part of Stacks.
//
@@ -38,25 +38,82 @@ using std::accumulate;
#include "MetaPopInfo.h"
#include "Vcf.h"
+struct MethylData {
+ uint16_t tot_depth;
+ uint16_t col;
+ methylt type;
+ MethylData() : tot_depth(0), col(0), type(methylt::irrelevant) {}
+ MethylData(uint16_t d, uint16_t c, methylt t) : tot_depth(d), col(c), type(t) {}
+};
+
+class MethylLoc {
+ vector<MethylData> _mdata;
+ uint16_t _index;
+ uint16_t _max_col;
+
+public:
+ MethylLoc() : _index(UINT16_MAX), _max_col(UINT16_MAX) {}
+ MethylLoc(uint16_t depth, uint16_t col, methylt type) {
+ _index = UINT16_MAX;
+ _max_col = col;
+ _mdata.push_back(MethylData(depth, col, type));
+ }
+ void reset() {
+ _index = UINT16_MAX;
+ }
+ void add(uint16_t depth, uint16_t col, methylt type) {
+ if (type == methylt::irrelevant)
+ return;
+
+ if (_max_col != UINT16_MAX) assert(col > _max_col);
+
+ _mdata.push_back(MethylData(depth, col, type));
+ _max_col = col;
+ return;
+ }
+ MethylData pos(uint16_t col) {
+ // Columns in _mdata are not contiguous, we only store sites with data.
+
+ // No sites for this locus.
+ if (_mdata.size() == 0 && _index == UINT16_MAX)
+ return MethylData(0, col, methylt::irrelevant);
+
+ if (_index == UINT16_MAX)
+ _index = 0;
+
+ if (col < _mdata[_index].col || col > _max_col)
+ return MethylData(0, col, methylt::irrelevant);
+
+ if (col == _mdata[_index].col) {
+ uint16_t ret_index = _index;
+ _index++;
+ return _mdata[ret_index];
+ }
+
+ return MethylData();
+ }
+};
+
class Datum {
public:
struct SNPData {
- size_t tot_depth;
+ size_t tot_depth;
Counts<Nt2> nt_depths;
- uint8_t gq;
- GtLiks gtliks;
+ uint8_t gq;
+ GtLiks gtliks;
SNPData() : tot_depth(0), gq(UINT8_MAX) {}
};
- int id; // Stack ID
- int merge_partner; // Stack ID of merged datum, if this datum was merged/phased from two, overlapping datums.
- int len; // Length of locus
- char *model; // String representing SNP model output for each nucleotide at this locus.
- char *gtype; // Mapping genotype
- char *cigar; // CIGAR string describing how the datum aligns to the catalog locus.
- vector<char *> obshap; // Observed Haplotypes
+ int id; // Stack ID
+ int merge_partner; // Stack ID of merged datum, if this datum was merged/phased from two, overlapping datums.
+ int len; // Length of locus
+ char *model; // String representing SNP model output for each nucleotide at this locus.
+ char *gtype; // Mapping genotype
+ char *cigar; // CIGAR string describing how the datum aligns to the catalog locus.
+ vector<char *> obshap; // Observed Haplotypes
vector<SNPData> snpdata;
-
+ MethylLoc methyldata;
+
Datum() {
this->id = -1;
this->gtype = NULL;
@@ -77,7 +134,8 @@ public:
if (g.length() == 0) return;
if (this->gtype != NULL) delete [] this->gtype;
this->gtype = new char [g.length() + 1];
- strcpy(this->gtype, g.c_str());
+ strncpy(this->gtype, g.c_str(), g.length());
+ this->gtype[g.length()] = '\0';
}
string genotype() { return string(this->gtype); }
};
@@ -258,10 +316,11 @@ void PopMap<LocusT>::populate_internal(
size_t ad_index = SIZE_MAX;
size_t gq_index = SIZE_MAX;
size_t gl_index = SIZE_MAX;
+ size_t my_index = SIZE_MAX;
for (auto& rec : vcf_records)
{ try {
- size_t col = rec.pos();
- bool snp_rec = !rec.is_monomorphic();
+ size_t col = rec.pos();
+ bool snp_rec = !rec.is_monomorphic();
if (snp_rec) {
if (!rec.is_snp()) {
cerr << "Error: Not a SNP.\n";
@@ -277,9 +336,18 @@ void PopMap<LocusT>::populate_internal(
ad_index = rec.index_of_gt_subfield("AD");
gq_index = rec.index_of_gt_subfield("GQ");
gl_index = rec.index_of_gt_subfield("GL");
+ if (vcf_header.methyl())
+ my_index = rec.index_of_gt_subfield("MY");
+
+ } else if (vcf_header.methyl()) {
+ assert(rec.count_formats() == 2 && strcmp(rec.format0(),"DP")==0);
+ dp_index = rec.index_of_gt_subfield("DP");
+ my_index = rec.index_of_gt_subfield("MY");
+
} else {
- assert(rec.count_formats() == 1 && strcmp(rec.format0(),"DP")==0);
- }
+ assert(rec.count_formats() == 1 && strcmp(rec.format0(),"DP")==0);
+ }
+
VcfRecord::iterator gt_itr = rec.begin_samples();
for (size_t sample_vcf_i = 0;
sample_vcf_i < vcf_header.samples().size();
@@ -334,6 +402,16 @@ void PopMap<LocusT>::populate_internal(
strncpy(d->obshap[0], "consensus", 10);
}
}
+
+ //
+ // Record methyltation status, if available.
+ //
+ if (vcf_header.methyl()) {
+ d->methyldata.add(VcfRecord::util::parse_gt_dp(gt_str, dp_index),
+ col,
+ VcfRecord::util::parse_gt_my(gt_str, my_index));
+ }
+
// Handle the non-SNP-record case.
if (!snp_rec) {
d->model[col] = 'O';
=====================================
src/PopSum.cc
=====================================
@@ -45,7 +45,7 @@ LocPopSum::~LocPopSum()
}
int
-LocPopSum::sum_pops(const CSLocus *cloc, Datum const*const* d, const MetaPopInfo &mpopi,
+LocPopSum::sum_pops(const CSLocus *cloc, Datum **d, const MetaPopInfo &mpopi,
bool verbose, ostream &log_fh)
{
uint len = strlen(cloc->con);
@@ -90,9 +90,17 @@ LocPopSum::sum_pops(const CSLocus *cloc, Datum const*const* d, const MetaPopInfo
this->tally_fixed_pos(cloc, d, s, k, pop.first_sample, pop.last_sample);
}
+ if (methyl_ann) {
+ for (uint k = 0; k < len; k++)
+ this->tally_methyl_pos(cloc, d, s, k, pop.first_sample, pop.last_sample);
+ for (uint k = pop.first_sample; k <= pop.last_sample; k++)
+ d[k]->methyldata.reset();
+
+ }
+
snp_cols.clear();
}
-
+
return 0;
}
@@ -347,6 +355,92 @@ LocPopSum::tally_heterozygous_pos(const CSLocus *cloc, Datum const*const* d, Loc
return 0;
}
+int
+LocPopSum::tally_methyl_pos(const CSLocus *cloc, Datum **d, LocSum *s,
+ int pos, uint start, uint end)
+{
+ s->nucs[pos].methyl_type(methylt::irrelevant);
+ s->nucs[pos].methyl_freq(0.0);
+
+ vector<size_t> methyl_calls (4, 0);
+ // methyl_calls[0] --> unmethyl_cpg
+ // methyl_calls[1] --> unmethyl_chg
+ // methyl_calls[2] --> unmethyl_chh
+ // methyl_calls[3] --> unmethyl_unk
+
+ // if (cloc->id == 13552) {
+ // cerr << "HERE\n";
+ // }
+
+ uint16_t num_indv = 0;
+ for (uint i = start; i <= end; i++) {
+ if (d[i] == NULL || pos >= d[i]->len)
+ continue;
+
+ //
+ // Pull any unmethylated marking from this position in this individual.
+ //
+ MethylData md = d[i]->methyldata.pos(pos);
+ switch(md.type) {
+ case methylt::unmethyl_cpg:
+ methyl_calls[0]++;
+ num_indv++;
+ break;
+ case methylt::unmethyl_chg:
+ methyl_calls[1]++;
+ num_indv++;
+ break;
+ case methylt::unmethyl_chh:
+ methyl_calls[2]++;
+ num_indv++;
+ break;
+ case methylt::unmethyl_unk:
+ methyl_calls[3]++;
+ num_indv++;
+ break;
+ default:
+ break;
+ }
+ }
+
+ //
+ // Determine how many alleles are present at this position in this population.
+ // We cannot deal with more than two alternative alleles, if there are more than two
+ // in a single population, print a warning and exclude this nucleotide position.
+ //
+ int methyl_cnt = 0;
+ for (size_t i = 0; i < 4; i++)
+ if (methyl_calls[i] > 0) methyl_cnt++;
+
+ methylt methyl_type = methylt::irrelevant;
+
+ switch (methyl_cnt) {
+ case 0:
+ return 0;
+ case 1:
+ if (methyl_calls[0] > 0)
+ methyl_type = methylt::unmethyl_cpg;
+ else if (methyl_calls[1] > 0)
+ methyl_type = methylt::unmethyl_chg;
+ else if (methyl_calls[2] > 0)
+ methyl_type = methylt::unmethyl_chh;
+ else
+ methyl_type = methylt::unmethyl_unk;
+ break;
+ default:
+ methyl_type = methylt::confounded;
+ break;
+ }
+
+ //
+ // Record the results in the PopSum object.
+ //
+ s->nucs[pos].methyl_type(methyl_type);
+ s->nucs[pos].methyl_freq((float) num_indv / (float) (end - start + 1));
+
+ return 0;
+}
+
double
LocPopSum::pi(double tot_alleles, double p, double q)
{
=====================================
src/PopSum.h
=====================================
@@ -1,6 +1,6 @@
// -*-mode:c++; c-style:k&r; c-basic-offset:4;-*-
//
-// Copyright 2011-2023, Julian Catchen <jcatchen at illinois.edu>
+// Copyright 2011-2024, Julian Catchen <jcatchen at illinois.edu>
//
// This file is part of Stacks.
//
@@ -37,6 +37,7 @@
#include "MetaPopInfo.h"
#include "Hwp.h"
+extern bool methyl_ann;
extern bool calc_hwp;
extern double minor_allele_freq;
extern corr_type fst_correction;
@@ -255,6 +256,8 @@ class SumStat: public PopStat {
};
bool _filtered_site;
uint16_t _num_indv;
+ methylt _methyl_type;
+ float _methyl_freq;
char _p_nuc;
HetNuc *_het_nuc;
@@ -264,6 +267,8 @@ public:
_num_indv = 0;
_p_nuc = 0;
_filtered_site = false;
+ _methyl_type = methylt::irrelevant;
+ _methyl_freq = 0.0;
}
~SumStat() {
if (this->_het_nuc != NULL)
@@ -328,6 +333,10 @@ public:
void exp_het(float exp_het) { if (this->_het_nuc != NULL) this->_het_nuc->_exp_het = exp_het; }
float exp_hom() { if (this->_het_nuc != NULL) return this->_het_nuc->_exp_hom; else return 1.0; }
void exp_hom(float exp_hom) { if (this->_het_nuc != NULL) this->_het_nuc->_exp_hom = exp_hom; }
+ methylt methyl_type() { return this->_methyl_type; }
+ void methyl_type(methylt t) { this->_methyl_type = t; }
+ float methyl_freq() { return this->_methyl_freq; }
+ void methyl_freq(float f) { this->_methyl_freq = f; }
bool filtered_site() { return this->_filtered_site; }
void filtered_site(bool v) { this->_filtered_site = v; }
@@ -479,7 +488,7 @@ public:
LocPopSum(size_t cloc_len, const MetaPopInfo& mpopi);
~LocPopSum();
- int sum_pops(const CSLocus *, Datum const*const*, const MetaPopInfo&, bool, ostream &);
+ int sum_pops(const CSLocus *, Datum **, const MetaPopInfo&, bool, ostream &);
int tally_metapop(const CSLocus *);
int calc_hapstats(const CSLocus *, const Datum **, const MetaPopInfo&);
const LocSum **all_pops() { return (const LocSum **) this->_per_pop; }
@@ -494,6 +503,7 @@ public:
private:
int tally_heterozygous_pos(const CSLocus *, Datum const*const*, LocSum *, int, int, uint, uint);
int tally_fixed_pos(const CSLocus *, Datum const*const*, LocSum *, int, uint, uint);
+ int tally_methyl_pos(const CSLocus *, Datum **, LocSum *, int, uint, uint);
int tally_ref_alleles(int, uint16_t &, char &, char &, uint16_t &, uint16_t &);
int tally_observed_haplotypes(const vector<char *> &, int);
LocStat *haplotype_diversity(int, int, Datum const*const*);
=====================================
src/Vcf.cc
=====================================
@@ -53,6 +53,29 @@ void VcfHeader::add_std_meta(const string& version) {
add_meta(VcfMeta("source", string("\"Stacks v") + VERSION + "\""));
+ add_meta(VcfMeta::predefs::info_AD);
+ add_meta(VcfMeta::predefs::info_AF);
+ add_meta(VcfMeta::predefs::info_DP);
+ add_meta(VcfMeta::predefs::info_NS);
+ add_meta(VcfMeta::predefs::format_AD);
+ add_meta(VcfMeta::predefs::format_DP);
+ add_meta(VcfMeta::predefs::format_HQ);
+ add_meta(VcfMeta::predefs::format_GL);
+ add_meta(VcfMeta::predefs::format_GQ);
+ add_meta(VcfMeta::predefs::format_GT);
+}
+
+void VcfHeader::add_methyl_meta(const string& version) {
+ add_meta(VcfMeta("fileformat", version));
+
+ time_t t;
+ time(&t);
+ char date[9];
+ strftime(date, 9, "%Y%m%d", localtime(&t));
+ add_meta(VcfMeta("fileDate", date));
+
+ add_meta(VcfMeta("source", string("\"Stacks v") + VERSION + "\""));
+
add_meta(VcfMeta::predefs::info_AD);
add_meta(VcfMeta::predefs::info_AF);
add_meta(VcfMeta::predefs::info_DP);
@@ -90,8 +113,33 @@ void VcfHeader::add_std_meta_with_contigs(const vector<Contig> &contigs, const s
add_meta(VcfMeta::predefs::format_GL);
add_meta(VcfMeta::predefs::format_GQ);
add_meta(VcfMeta::predefs::format_GT);
- add_meta(VcfMeta::predefs::format_MY);
+}
+
+void VcfHeader::add_methyl_meta_with_contigs(const vector<Contig> &contigs, const string& version) {
+ add_meta(VcfMeta("fileformat", version));
+ time_t t;
+ time(&t);
+ char date[9];
+ strftime(date, 9, "%Y%m%d", localtime(&t));
+ add_meta(VcfMeta("fileDate", date));
+
+ add_meta(VcfMeta("source", string("\"Stacks v") + VERSION + "\""));
+
+ for (auto &ctg: contigs)
+ add_meta(VcfMeta("contig", "<ID=" + ctg.name + ",length=" + ctg.length + ">"));
+
+ add_meta(VcfMeta::predefs::info_AD);
+ add_meta(VcfMeta::predefs::info_AF);
+ add_meta(VcfMeta::predefs::info_DP);
+ add_meta(VcfMeta::predefs::info_NS);
+ add_meta(VcfMeta::predefs::format_AD);
+ add_meta(VcfMeta::predefs::format_DP);
+ add_meta(VcfMeta::predefs::format_HQ);
+ add_meta(VcfMeta::predefs::format_GL);
+ add_meta(VcfMeta::predefs::format_GQ);
+ add_meta(VcfMeta::predefs::format_GT);
+ add_meta(VcfMeta::predefs::format_MY);
}
void VcfRecord::assign(const char* rec, size_t len, const VcfHeader& header) {
@@ -228,6 +276,40 @@ size_t VcfRecord::util::parse_gt_dp(
return dp;
}
+methylt VcfRecord::util::parse_gt_my(
+ const char* gt_str,
+ size_t my_index
+) {
+ const char* p = VcfRecord::util::find_gt_subfield(gt_str, my_index);
+ if (p == NULL) {
+ cerr << "Error: MY field is missing.\n";
+ throw exception();
+ }
+ methylt my;
+
+ switch(*p) {
+ case '.':
+ my = methylt::irrelevant;
+ break;
+ case 'z':
+ my = methylt::unmethyl_cpg;
+ break;
+ case 'x':
+ my = methylt::unmethyl_chg;
+ break;
+ case 'h':
+ my = methylt::unmethyl_chh;
+ break;
+ case 'u':
+ my = methylt::unmethyl_unk;
+ break;
+ default:
+ cerr << "Error: Bad MY field.\n";
+ throw exception();
+ }
+ return my;
+}
+
Counts<Nt2>
VcfRecord::util::parse_gt_ad(
const char* gt_str,
@@ -409,4 +491,12 @@ VcfParser::read_header()
p = next;
} while (p != end);
}
+
+ //
+ // Check if the VCF header contained a definition of methylated data, e.g.
+ // ##FORMAT=<ID=MY,Number=1,Type=String,Description="Methylation Annotation">
+ //
+ for (auto m: header_.meta())
+ if (m.key() == "FORMAT" && m.value().substr(4,2) == "MY")
+ header_.methyl(true);
}
=====================================
src/Vcf.h
=====================================
@@ -1,6 +1,6 @@
// -*-mode:c++; c-style:k&r; c-basic-offset:4;-*-
//
-// Copyright 2010-2023, Julian Catchen <jcatchen at illinois.edu>
+// Copyright 2010-2024, Julian Catchen <jcatchen at illinois.edu>
//
// This file is part of Stacks.
//
@@ -21,6 +21,7 @@
#ifndef __VCF_H__
#define __VCF_H__
+#include "stacks.h"
#include "constants.h"
#include "nucleotides.h"
#include "utils.h"
@@ -67,14 +68,15 @@ public:
* Stores the contents of a VCF header.
*/
class VcfHeader {
- vector<string> samples_;
- vector<VcfMeta> meta_;
+ vector<string> samples_;
+ vector<VcfMeta> meta_;
map<string, size_t> sample_indexes_;
-
+ bool contains_methylation_;
+
template<typename OStream> void print(OStream& os) const; // Template because VersatileWriter isn't a proper std::ostream.
public:
- VcfHeader() : samples_(), meta_(), sample_indexes_() {}
+ VcfHeader() : samples_(), meta_(), sample_indexes_(), contains_methylation_(false) {}
const vector<VcfMeta>& meta() const {return meta_;}
const vector<string>& samples() const {return samples_;}
@@ -83,11 +85,18 @@ public:
void add_meta(const VcfMeta& m) {meta_.push_back(m);}
void add_sample(const string& s) {samples_.push_back(s); sample_indexes_.insert({s, samples_.size()-1});}
+ const bool methyl() const { return this->contains_methylation_; }
+ void methyl(const bool methyl) { this->contains_methylation_ = methyl; }
+
// Creates a standard header.
void add_std_meta(const string& version = "VCFv4.2");
+ // Creates a standard header with methylation.
+ void add_methyl_meta(const string& version = "VCFv4.2");
// Creates a standard header with contigs defined.
void add_std_meta_with_contigs(const vector<Contig> &, const string& version = "VCFv4.2");
+ // Creates a standard header with methylation and contigs defined.
+ void add_methyl_meta_with_contigs(const vector<Contig> &, const string& version = "VCFv4.2");
static const string std_fields;
@@ -190,7 +199,7 @@ public:
static const char allele_sep = ',';
static const char filter_sep = ';';
- static const char info_sep = ';';
+ static const char info_sep = ';';
static const char format_sep = ':';
static const char sample_sep = ':';
@@ -203,6 +212,7 @@ public:
static Counts<Nt2> parse_gt_ad(const char* gt_str, size_t ad_index, const vector<Nt2>& alleles);
static uint8_t parse_gt_gq(const char* gt_str, size_t gq_index);
static GtLiks parse_gt_gl(const char* gt_str, size_t gl_index, const vector<Nt2>& alleles);
+ static methylt parse_gt_my(const char* gt_str, size_t my_index);
static const char* find_gt_subfield(const char* sample, size_t n);
static void skip_gt_subfields(const char** start, size_t n);
=====================================
src/clean.cc
=====================================
@@ -697,13 +697,20 @@ correct_barcode(set<string> &bcs, RawRead *href, seqt type, int num_errs)
// Functions for filtering adapter sequence
//
int
-init_adapter_seq(int kmer_size, char *adapter, int &adp_len, AdapterHash &kmers)
+init_adapter_seq(int &kmer_size, char *adapter, int &adp_len, int adp_mm_dist, AdapterHash &kmers)
{
+ //
+ // Determine k-mer size, maxing out at k = 11 if the adapter is long enough.
+ //
+ adp_len = strlen(adapter);
+ kmer_size = determine_kmer_length(adp_len, adp_mm_dist);
+
+ if (kmer_size > 9) kmer_size = 9;
+
string kmer;
- adp_len = strlen(adapter);
+ int num_kmers = adp_len - kmer_size + 1;
+ char *p = adapter;
- int num_kmers = adp_len - kmer_size + 1;
- char *p = adapter;
for (int i = 0; i < num_kmers; i++) {
kmer.assign(p, kmer_size);
kmers[kmer].push_back(i);
@@ -715,14 +722,14 @@ init_adapter_seq(int kmer_size, char *adapter, int &adp_len, AdapterHash &kmers)
int
filter_adapter_seq(RawRead *href, char *adapter, int adp_len, AdapterHash &adp_kmers,
- int kmer_size, int distance, int len_limit)
+ int kmer_size, int adp_mm_dist, int len_limit)
{
vector<pair<int, int> > hits;
int query_stop = href->inline_bc_len;
int num_kmers = href->len - query_stop - kmer_size + 1;
const char *p = href->seq + query_stop;
string kmer;
-
+
//
// Identify matching kmers and their locations of occurance.
//
@@ -732,7 +739,7 @@ filter_adapter_seq(RawRead *href, char *adapter, int adp_len, AdapterHash &adp_k
if (adp_kmers.count(kmer) > 0) {
for (uint j = 0; j < adp_kmers[kmer].size(); j++) {
// cerr << "Kmer hit " << kmer << " at query position " << i << " at hit position " << adp_kmers[kmer][j] << "\n";
- hits.push_back(make_pair(i, adp_kmers[kmer][j]));
+ hits.push_back(make_pair( (p - href->seq), adp_kmers[kmer][j]));
}
}
p++;
@@ -762,14 +769,14 @@ filter_adapter_seq(RawRead *href, char *adapter, int adp_len, AdapterHash &adp_k
j--;
}
- if (mismatches > distance)
+ if (mismatches > adp_mm_dist)
continue;
start_pos = i + 1;
i = hits[k].first;
j = hits[k].second;
- while (i < (int) href->len && j < adp_len && mismatches <= distance) {
+ while (i < (int) href->len && j < adp_len && mismatches <= adp_mm_dist) {
if (href->seq[i] != adapter[j])
mismatches++;
i++;
@@ -779,7 +786,7 @@ filter_adapter_seq(RawRead *href, char *adapter, int adp_len, AdapterHash &adp_k
// cerr << "Starting position: " << start_pos << "; Query end (i): " << i << "; adapter end (j): " << j
// << "; number of mismatches: " << mismatches << "; Seq Len: " << href->len << "; SeqSeq Len: " << strlen(href->seq) << "\n";
- if (mismatches <= distance && (i == (int) href->len || j == adp_len)) {
+ if (mismatches <= adp_mm_dist && (i == (int) href->len || j == adp_len)) {
// cerr << " Trimming or dropping.\n";
if (start_pos < len_limit) {
return 0;
=====================================
src/clean.h
=====================================
@@ -403,7 +403,7 @@ int reverse_qual(char *, int, bool);
bool correct_barcode(set<string> &, RawRead *, seqt, int);
int filter_adapter_seq(RawRead *, char *, int, AdapterHash &, int, int, int);
-int init_adapter_seq(int, char *, int &, AdapterHash &);
+int init_adapter_seq(int &, char *, int &, int, AdapterHash &);
int check_quality_scores(RawRead *, int, int, int, int);
int check_poly_g_run(RawRead *, int, int);
=====================================
src/export_formats.cc
=====================================
@@ -385,6 +385,89 @@ HapstatsExport::write_batch(const vector<LocBin *> &loci)
return 0;
}
+int
+MethylSitesExport::open(const MetaPopInfo *mpopi)
+{
+ this->_path = out_path + out_prefix + ".methylsites.tsv";
+ this->_mpopi = mpopi;
+ this->_pop_cnt = this->_mpopi->pops().size();
+
+ this->_fh.open(this->_path.c_str(), ofstream::out);
+ check_open(this->_fh, this->_path);
+ this->_fh.precision(fieldw);
+ this->_fh.setf(std::ios::fixed);
+
+ cout << "Population-level methylation statistics will be written to '" << this->_path << "'\n";
+
+ return 0;
+}
+
+int
+MethylSitesExport::write_header()
+{
+ //
+ // Write the population members.
+ //
+ for (auto& pop : this->_mpopi->pops()) {
+ this->_fh << "# " << pop.name << "\t";
+ for (size_t i = pop.first_sample; i <= pop.last_sample; i++) {
+ this->_fh << this->_mpopi->samples()[i].name;
+ if (i < pop.last_sample)
+ this->_fh << ",";
+ }
+ this->_fh << "\n";
+ }
+
+ this->_fh << "# Locus ID" << "\t"
+ << "Chr" << "\t"
+ << "BP" << "\t"
+ << "Col" << "\t"
+ << "Pop ID" << "\t"
+ << "N" << "\t"
+ << "MethylType" << "\t"
+ << "MethylFreq" << "\n";
+ return 0;
+}
+
+const std::string MethylSitesExport::typestrs[] = {"CPG", "CHG", "CHH", "UNK"};
+
+int
+MethylSitesExport::write_batch(const vector<LocBin *> &loci)
+{
+ CSLocus *cloc;
+ const LocSum *s;
+ string mtype;
+
+ for (uint i = 0; i < loci.size(); i++) {
+ cloc = loci[i]->cloc;
+
+ for (uint pos = 0; pos < cloc->len; pos++) {
+
+ for (uint pop = 0; pop < this->_pop_cnt; pop++) {
+
+ s = loci[i]->s->per_pop(pop);
+
+ if (s->nucs[pos].num_indv() == 0 ||
+ s->nucs[pos].methyl_type() == methylt::confounded ||
+ s->nucs[pos].methyl_type() == methylt::irrelevant)
+ continue;
+
+ this->_fh
+ << cloc->id << "\t"
+ << cloc->loc.chr() << "\t"
+ << cloc->sort_bp(pos) + 1 << "\t"
+ << pos << "\t"
+ << this->_mpopi->pops()[pop].name << "\t"
+ << s->nucs[pos].num_indv() << "\t"
+ << this->typestrs[s->nucs[pos].methyl_type()] << "\t"
+ << std::setprecision(fieldw) << s->nucs[pos].methyl_freq() << "\n";
+ }
+ }
+ }
+
+ return 0;
+}
+
SnpDivergenceExport::SnpDivergenceExport(ofstream &log_fh) : _mpopi(NULL), _order(NULL)
{
if (ordered_export)
=====================================
src/export_formats.h
=====================================
@@ -1,6 +1,6 @@
// -*-mode:c++; c-style:k&r; c-basic-offset:4;-*-
//
-// Copyright 2012-2022, Julian Catchen <jcatchen at illinois.edu>
+// Copyright 2012-2024, Julian Catchen <jcatchen at illinois.edu>
//
// This file is part of Stacks.
//
@@ -167,6 +167,22 @@ class HapstatsExport: public Export {
int write_batch(const vector<LocBin *> &);
};
+class MethylSitesExport: public Export {
+ //
+ // Output the locus-level methylation statistics.
+ //
+ const MetaPopInfo *_mpopi;
+ uint _pop_cnt;
+ static const std::string typestrs[];
+
+ public:
+ MethylSitesExport() : _mpopi(NULL), _pop_cnt(UINT_MAX) {}
+ ~MethylSitesExport() {}
+ int open(const MetaPopInfo *mpopi);
+ int write_header();
+ int write_batch(const vector<LocBin *> &);
+};
+
class SnpDivergenceExport: public Export {
//
// Output the SNP-level divergence statistics.
=====================================
src/gstacks.cc
=====================================
@@ -1,6 +1,6 @@
// -*-mode:c++; c-style:k&r; c-basic-offset:4;-*-
//
-// Copyright 2017-2023, Julian Catchen <jcatchen at illinois.edu>
+// Copyright 2017-2024, Julian Catchen <jcatchen at illinois.edu>
//
// This file is part of Stacks.
//
@@ -191,7 +191,11 @@ try {
check_open(o_gzfasta_f, o_gzfasta_path);
VcfHeader vcf_header;
- vcf_header.add_std_meta();
+
+ call_methyl_status ?
+ vcf_header.add_methyl_meta() :
+ vcf_header.add_std_meta();
+
for(size_t s : bam_mpopi->sample_indexes_orig_order())
vcf_header.add_sample(bam_mpopi->samples()[s].name);
o_vcf_f.reset(new VcfWriter(out_dir + "catalog.calls", move(vcf_header)));
@@ -2449,16 +2453,21 @@ void LocusProcessor::call_methylated_status (
char *ref = new char[aln_loc.ref().length() + 1];
const char *r = this->ref_chrs_[loc.chr()].c_str() + loc.bp;
- cerr << "Length: " << aln_loc.ref().length() << "\n";
+
+ // cerr << "Loc Length: " << aln_loc.ref().length() << "\n";
+ // cerr << "Chr Length: " << this->ref_chrs_[loc.chr()].length() << "\n";
+
//
// Pull a copy of the locus from the reference genome.
//
if (loc.strand == strand_type::strand_plus) {
strncpy(ref, r, aln_loc.ref().length());
+ ref[aln_loc.ref().length()] = '\0';
} else {
// If the locus is on the negative strand
r = r - (aln_loc.ref().length() - 1);
strncpy(ref, r, aln_loc.ref().length());
+ ref[aln_loc.ref().length()] = '\0';
rev_comp_inplace(ref);
}
@@ -2482,10 +2491,10 @@ void LocusProcessor::call_methylated_status (
aligner.init(aln_loc.ref().length(), aln_loc.ref().length());
aligner.align(string(ref), consensus.str());
string cigar_str = invert_cigar(aligner.result().cigar);
- cerr << "CIGAR: " << cigar_str << "\n";
- cerr << "REF: " << string(ref) << "\n";
- cerr << "LOCUS: " << consensus.str() << "\n";
-
+
+ // cerr << "CIGAR: " << cigar_str << "\n";
+ // cerr << "REF: " << string(ref) << "\n";
+ // cerr << "LOCUS: " << consensus.str() << "\n";
// cerr << "RAD locus is at " << loc.chr() << "; "
// << (loc.strand == strand_type::strand_plus ? loc.bp : loc.bp - aln_loc.ref().length() - 1) << ": "
// << string(ref, aln_loc.ref().length()) << "\n"
@@ -2498,8 +2507,6 @@ void LocusProcessor::call_methylated_status (
size_t end = calls.size() - 1;
for (size_t i = 0; i < calls.size(); i++) {
- const vector<SampleCall> sample_calls = calls[i].sample_calls();
-
// Initialize the array of calls at this site.
methylcalls.push_back(SiteMethylCounts());
for (size_t j = 0; j < tot_samples; j++)
@@ -2524,7 +2531,9 @@ void LocusProcessor::call_methylated_status (
// We will see the 'C' as a 'G', converted by EM-seq to an 'A'
//
- if (i < end - 2) {
+ if (i < end - 2 &&
+ calls[i + 1].alleles().empty() == false &&
+ calls[i + 2].alleles().empty() == false) {
// Are there two additional sites left in the locus, so we can call CHH and CHG?
vector<bool> site_1(tot_samples, false);
vector<bool> site_2(tot_samples, false);
@@ -2543,7 +2552,8 @@ void LocusProcessor::call_methylated_status (
methylcalls[i].samples[j] = methylt::unmethyl_cpg;
}
- } else if (i < end - 1) {
+ } else if (i < end - 1 &&
+ calls[i + 1].alleles().empty() == false) {
//
// Is there one additional site left in the locus, so we can call CpG?
// If so:
@@ -2600,6 +2610,9 @@ void LocusProcessor::call_methylated_status (
inline
void LocusProcessor::sites_equal_nucleotide(const SiteCall &call, char nuc, vector<bool> &site_vals)
{
+ if (call.alleles().size() == 0)
+ return;
+
if (call.alleles().size() == 1) {
// Fixed site
if (call.most_frequent_allele() == nuc)
=====================================
src/populations.cc
=====================================
@@ -34,6 +34,7 @@ using namespace std;
// Global variables to hold command-line options.
InputMode input_mode = InputMode::stacks2;
int num_threads = 1;
+bool methyl_ann = false; // Does the catalog contain methylation annotations?
bool quiet = false;
string in_path;
string in_vcf_path;
@@ -231,6 +232,9 @@ try {
exports.push_back(new SumstatsExport());
exports.push_back(new HapstatsExport());
+ if (methyl_ann)
+ exports.push_back(new MethylSitesExport());
+
SnpDivergenceExport *sdiv_exp = NULL;
HapDivergenceExport *hdiv_exp = NULL;
if (calc_fstats) {
@@ -636,6 +640,12 @@ BatchLocusProcessor::init_stacks_loci(string in_path, string pmap_path)
this->_fasta_reader.open(catalog_fa_path);
this->_cloc_reader.open(catalog_vcf_path);
+ //
+ // Did we find methylation annotations in the catalog.calls file?
+ //
+ if (this->_cloc_reader.header().methyl())
+ methyl_ann = true;
+
// Create the population map or check that all samples have data.
if (pmap_path.empty()) {
this->_mpopi->init_names(this->cloc_reader().header().samples());
=====================================
src/process_radtags.cc
=====================================
@@ -97,8 +97,9 @@ uint max_bc_size_2 = 0;
//
// Kmer data for adapter filtering.
//
-int kmer_size = 5;
-int distance = 1;
+int kmer_size_1 = 11;
+int kmer_size_2 = 11;
+int adp_mm_dist = 1;
int adp_1_len = 0;
int adp_2_len = 0;
AdapterHash adp_1_kmers, adp_2_kmers;
@@ -162,15 +163,15 @@ int main (int argc, char* argv[]) {
if (filter_adapter) {
cerr << "Filtering reads for adapter sequence:\n";
if (adapter_1 != NULL) {
+ init_adapter_seq(kmer_size_1, adapter_1, adp_1_len, adp_mm_dist, adp_1_kmers);
cerr << " " << adapter_1 << "\n";
- init_adapter_seq(kmer_size, adapter_1, adp_1_len, adp_1_kmers);
}
if (adapter_2 != NULL) {
+ init_adapter_seq(kmer_size_2, adapter_2, adp_2_len, adp_mm_dist, adp_2_kmers);
cerr << " " << adapter_2 << "\n";
- init_adapter_seq(kmer_size, adapter_2, adp_2_len, adp_2_kmers);
}
- cerr << " " << ::distance << " mismatches allowed to adapter sequence.\n";
+ cerr << " " << adp_mm_dist << " mismatches allowed to adapter sequence.\n";
}
vector<pair<string, string> > files;
@@ -526,7 +527,7 @@ process_paired_reads(string prefix_1,
parse_input_record(s_2, r_2);
counter["total"] += 2;
- if (force_poly_g == false && r_1->check_poly_g()) check_poly_g = true;
+ if (force_poly_g == false && clean == true && r_1->check_poly_g()) check_poly_g = true;
//
// If a BestRAD protocol was used, check which read the barcode/restriction cutsite is on
@@ -1032,8 +1033,8 @@ process_paired_reads_parallel(string prefix_1,
parse_input_record(s_2, r_2);
cntr["total"] += 2;
- if (force_poly_g == false && r_1->check_poly_g()) check_poly_g = true;
-
+ if (force_poly_g == false && clean == true && r_1->check_poly_g()) check_poly_g = true;
+
//
// If a BestRAD protocol was used, check which read the barcode/restriction cutsite is on
// and transpose the reads if necessary.
@@ -1232,7 +1233,7 @@ process_reads(string prefix,
parse_input_record(s, r);
- if (force_poly_g == false && r->check_poly_g()) check_poly_g = true;
+ if (force_poly_g == false && clean == true && r->check_poly_g()) check_poly_g = true;
if (barcode_type == inline_null ||
barcode_type == index_null)
@@ -1599,8 +1600,8 @@ process_reads_parallel(string prefix,
parse_input_record(s, r);
- if (force_poly_g == false && r->check_poly_g()) check_poly_g = true;
-
+ if (force_poly_g == false && clean == true && r->check_poly_g()) check_poly_g = true;
+
bc = new BarcodePair();
//
// If no barcodes were specified, set the barcode object to be the input file name so
@@ -1757,7 +1758,8 @@ process_singlet(RawRead *href,
// Either the user has forced the check on, and check_poly_g is true, or we turned it on
// internally via href->check_poly_g because of the machine type that generated the data.
//
- if ((check_poly_g || href->check_poly_g()) &&
+ //if ((check_poly_g || href->check_poly_g()) &&
+ if (check_poly_g &&
check_poly_g_run(href, href->inline_bc_len, len_limit) <= 0) {
counter["poly_g"]++;
if (barcode_type != null_null)
@@ -1773,10 +1775,10 @@ process_singlet(RawRead *href,
int res = 1;
if (paired_end == true && adp_2_len > 0)
res = filter_adapter_seq(href, adapter_2, adp_2_len, adp_2_kmers,
- kmer_size, ::distance, len_limit);
+ kmer_size_2, adp_mm_dist, len_limit);
if (paired_end == false && adp_1_len > 0)
res = filter_adapter_seq(href, adapter_1, adp_1_len, adp_1_kmers,
- kmer_size, ::distance, len_limit);
+ kmer_size_1, adp_mm_dist, len_limit);
if (res <= 0) {
// cerr << "Sequence " << href->seq << " contains adapter.\n";
counter["adapter"]++;
@@ -2425,7 +2427,7 @@ int parse_command_line(int argc, char* argv[]) {
filter_adapter = true;
break;
case 'T':
- ::distance = is_integer(optarg);
+ adp_mm_dist = is_integer(optarg);
break;
case 'H':
retain_header = true;
=====================================
src/process_radtags.h
=====================================
@@ -1,6 +1,6 @@
// -*-mode:c++; c-style:k&r; c-basic-offset:4;-*-
//
-// Copyright 2010-2022, Julian Catchen <jcatchen at illinois.edu>
+// Copyright 2010-2024, Julian Catchen <jcatchen at illinois.edu>
//
// This file is part of Stacks.
//
=====================================
src/process_shortreads.cc
=====================================
@@ -81,10 +81,11 @@ uint max_bc_size_2 = 0;
//
// Kmer data for adapter filtering.
//
-int kmer_size = 5;
-int distance = 1;
-int adp_1_len = 0;
-int adp_2_len = 0;
+int kmer_size_1 = 11;
+int kmer_size_2 = 11;
+int adp_mm_dist = 1;
+int adp_1_len = 0;
+int adp_2_len = 0;
AdapterHash adp_1_kmers, adp_2_kmers;
int main (int argc, char* argv[]) {
@@ -112,13 +113,13 @@ int main (int argc, char* argv[]) {
cerr << "Filtering reads for adapter sequence:\n";
if (adapter_1 != NULL) {
cerr << " " << adapter_1 << "\n";
- init_adapter_seq(kmer_size, adapter_1, adp_1_len, adp_1_kmers);
+ init_adapter_seq(kmer_size_1, adapter_1, adp_1_len, adp_mm_dist, adp_1_kmers);
}
if (adapter_2 != NULL) {
cerr << " " << adapter_2 << "\n";
- init_adapter_seq(kmer_size, adapter_2, adp_2_len, adp_2_kmers);
+ init_adapter_seq(kmer_size_2, adapter_2, adp_2_len, adp_mm_dist, adp_2_kmers);
}
- cerr << " " << distance << " mismatches allowed to adapter sequence.\n";
+ cerr << " " << adp_mm_dist << " mismatches allowed to adapter sequence.\n";
}
vector<pair<string, string> > files;
@@ -631,10 +632,10 @@ process_singlet(RawRead *href,
int res = 1;
if (paired_end == true && adp_2_len > 0)
res = filter_adapter_seq(href, adapter_2, adp_2_len, adp_2_kmers,
- kmer_size, distance, len_limit);
+ kmer_size_2, adp_mm_dist, len_limit);
if (paired_end == false && adp_1_len > 0)
res = filter_adapter_seq(href, adapter_1, adp_1_len, adp_1_kmers,
- kmer_size, distance, len_limit);
+ kmer_size_1, adp_mm_dist, len_limit);
if (res == 0) {
counter["adapter"]++;
href->retain = 0;
@@ -1014,7 +1015,7 @@ int parse_command_line(int argc, char* argv[]) {
filter_adapter = true;
break;
case 'T':
- distance = is_integer(optarg);
+ adp_mm_dist = is_integer(optarg);
break;
case 'L':
len_limit = is_integer(optarg);
=====================================
src/stacks.h
=====================================
@@ -1,6 +1,6 @@
// -*-mode:c++; c-style:k&r; c-basic-offset:4;-*-
//
-// Copyright 2010-2023, Julian Catchen <jcatchen at illinois.edu>
+// Copyright 2010-2024, Julian Catchen <jcatchen at illinois.edu>
//
// This file is part of Stacks.
//
@@ -47,7 +47,7 @@ enum snp_type {snp_type_het, snp_type_hom, snp_type_unk, snp_type_discarded};
enum read_type {primary, secondary};
enum searcht {sequence, genomic_loc};
enum corr_type {p_value, bonferroni_win, bonferroni_gen, no_correction};
-enum methylt {unmethyl_cpg, unmethyl_chg, unmethyl_chh, unmethyl_unk, irrelevant};
+enum methylt {unmethyl_cpg, unmethyl_chg, unmethyl_chh, unmethyl_unk, confounded, irrelevant};
class SNP {
public:
View it on GitLab: https://salsa.debian.org/med-team/stacks/-/commit/f867aeed77af01f09efbe89dcab096843cddaf81
--
View it on GitLab: https://salsa.debian.org/med-team/stacks/-/commit/f867aeed77af01f09efbe89dcab096843cddaf81
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